Macs in Chemistry

Insanely Great Science

data analysis

DataWarrior Updated

 

I notice that DataWarrior has had a couple of updates recently.

DataWarrior combines dynamic graphical views and interactive row filtering with chemical intelligence. Scatter plots, box plots, bar charts and pie charts not only visualize numerical or category data, but also show trends of multiple scaffolds or compound substitution patterns.

The latest updates

v04.06.01: August 2017 Fixed plugin interface bug. Various small bug-fixes and improvements.
v04.06.00: July 2017 new plugin interface to easily develop database access extentions

DataWarrior can be downloaded here http://www.openmolecules.org/datawarrior/download.html.


Comments

Flot plots updated

 

I have updated the page showing the interactive plots using Flot and ChemDoodle Web Components

I have a regular need to share results from my work and historically this has been via a paper reports that have more recently been replaced by electronic versions. Whilst useful, these reports lack the interactivity, in particular it is extremely useful to be able to easily link data points on a scatter plot with the corresponding chemical structure. So I’ve started using web-based reports to add extra functionality. Unfortunately it has often required the addition of applets or plugins that I can’t be sure the viewer will have available so with the advent of HTML5 I’ve been exploring writing the reports using just HTML and javascript. One of the major challenges is to produce interactive plots instead of using static images, and I’ve been exploring the use of Flot to produce a plot with chemical structures produced using either a web-service like ChemSpider or a javascript library of web components developed by ChemDoodle.

flot


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Free machine learning and data science ebooks

 

An interesting post By Matthew Mayo, KDnuggets.

Here is a quick collection of such books to start your fair weather study off on the right foot. The list begins with a base of statistics, moves on to machine learning foundations, progresses to a few bigger picture titles, has a quick look at an advanced topic or 2, and ends off with something that brings it all together. A mix of classic and contemporary titles, hopefully you find something new (to you) and of interest here.


Comments

StarDrop 6.4

 

StarDrop 6.4 now links prepared 3D docking and alignment models with data visualisation, 2D SAR analyses and predictive models in a single interface.

Computational chemists can make their validated 3D models available to their colleagues via StarDrop’s Pose Generation Interface, which is compatible with software from major computational chemistry providers, including:

  • FlexX™ – BioSolveIT
  • Gold™ – Cambridge Crystallographic Data Centre
  • MOE™ – Chemical Computing Group
  • AutoDock Vina – The Scripps Research Institute
  • POSIT™ – OpenEye Scientific
  • …extendable to other third party applications.

The Pose Generation Interface communicates with a Pose Generation Server, on which computational chemists can easily publish their validated docking or 3D alignment models. These are made instantly available for StarDrop users to submit their compounds and the resulting poses, protein structures and scores are returned directly to StarDrop for visualisation and analysis.

The Pose Generation Server can be installed wherever you run your 3D modelling software, supporting Linux, Windows® and Mac®

There are more details in the poster presented at the Spring ACS 2017.


Comments

Data Extractor updated

 

The Data Analysis Tools page contains a list of applications for data analysis that run under Mac OSX, in addition I've also included some other useful tools. Included in the list is Data Extractor.

Data Extractor allows to extract data in a sparse format contained inside various files and collect the data you need in an internal structured table. Collected data can be exported at any time in various format (CSV, TSV, HTML, Custom). Data extractor can parse thousands and thousands of file in few seconds and collect the data inside. It uses simple smart instructions about how to recognize the data you need, how to extract them and where to put these data inside a structured table, ready to be exported.

Version 1.5 updates:

  • Additional force option: 'Prefix at Start of Line'
  • Extraction algorithm improved
  • Bug fix extracting data with start tag having a space as first character
  • Other minor bug fix
  • Optimized for macOS 10.12 Sierra

Comments

Scaffold Hunter update

 

Scaffold Hunter is a chemical data organization and analysis tool and that has been continuously enhanced since the start of its development in 2007. The platform-independent open-source tool was first released in 2009 and provided an interactive visualisation of the so-called scaffold tree, which is a hierarchical classification scheme for molecules based on their common scaffolds. A recent publication describes recent extensions that significantly increase the applicability for a variety of tasks DOI.

When I first opened the application I did not find it particularly intuitive, fortunately there is a online tutorial and sample datasets available.


Comments

Expressions

 

I've just been sent details of an app to aid generating regular expressions, Expressions. I use BBEdit for most of my regular expression searching but this looks a brilliant way to build the query.

screen800x500


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Vortex does Biology

 

I was at the Dotmatics UGM recently and they gave an insight into some of the future directions. One of the areas under consideration is the use of Vortex support for Biological data analysis.

Vortex is a very high performance data analysis and plotting tool, capable of handling many millions of rows of data. It also has chemical intelligence built in, allowing structure-based searching, physicochemical properties calculation, clustering and match pair analysis.

The support for biology is a new addition and I've written a brief review here.

sequaligned

Added to the growing list of software reviews.


Comments

Swift Algorithm Club

 

The Swift Algorithm Club is a new site that described implementations of popular algorithms and data structures in Swift. However there is also an added bonus in that there are also detailed explanations of how they work. The list below gives an idea of what is available or under construction, and I’m sure they would be delighted to receive contributions.

The algorithms

Searching

  • Linear Search. Find an element in an array.
  • Binary Search. Quickly find elements in a sorted array.
  • Count Occurrences. Count how often a value appears in an array.
  • Select Minimum / Maximum. Find the minimum/maximum value in an array.
  • k-th Largest Element. Find the k-th largest element in an array, such as the median.
  • Selection Sampling. Randomly choose a bunch of items from a collection.
  • Union-Find. Keeps track of disjoint sets and lets you quickly merge them.

String Search

  • Brute-Force String Search. A naive method.
  • Boyer-Moore. A fast method to search for substrings. It skips ahead based on a look-up table, to avoid looking at every character in the text.
  • Knuth-Morris-Pratt
  • Rabin-Karp
  • Longest Common Subsequence. Find the longest sequence of characters that appear in the same order in both strings.

Sorting

It's fun to see how sorting algorithms work, but in practice you'll almost never have to provide your own sorting routines. Swift's own sort() is more than up to the job. But if you're curious, read on...

Basic sorts:

  • Insertion Sort
  • Selection Sort
  • Shell Sort

Fast sorts:

  • Quicksort
  • Merge Sort
  • Heap Sort

Special-purpose sorts:

  • Counting Sort
  • Radix Sort
  • Topological Sort

Bad sorting algorithms (don't use these!):

  • Bubble Sort

Compression

  • Run-Length Encoding (RLE). Store repeated values as a single byte and a count.
  • Huffman Coding. Store more common elements using a smaller number of bits.

Miscellaneous

  • Shuffle. Randomly rearranges the contents of an array.
  • Comb Sort. An improve upon the Bubble Sort algorithm.

Mathematics

  • Greatest Common Divisor (GCD). Special bonus: the least common multiple.
  • Permutations and Combinations. Get your combinatorics on!
  • Shunting Yard Algorithm. Convert infix expressions to postfix.
  • Statistics

Machine learning

  • k-Means Clustering. Unsupervised classifier that partitions data into k clusters.
  • k-Nearest Neighbors
  • Linear Regression
  • Logistic Regression
  • Neural Networks
  • PageRank

Comments

Importing Open Source Malaria Data into DataWarrior

 

Thomas Sander from openmolecules.org has provided a version of DataWarrior that can directly import the Open Source Malaria Data.

The new version can be downloaded here http://www.openmolecules.org/datawarrior, once downloaded and you will need to temporarily adjust your security settings to open it the first time. This is because DataWarrior is not from the Mac App Store or an identified developer. Once open make sure you reset your security settings.

security

Once installed and opened select the macro as shown below to retrieve the Open Source Malaria Data.

screen

The import only takes a few seconds and pulls the data directly from the Open Source Malaria spreadsheet so it will contains the latest information.

DataWarrior

There are now a variety of different options for accessing the Open Source Malaria data you can use the Cheminfo spreadsheet, or use a Vortex script or even an iPython notebook.


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MathStatica 2.72

 

mathStatica 2.72 is fully compatible with Mathematica 11

mathStatica 2.7 unleashes the power of your computer — automatically — featuring phenomenal speed and power for users with multi-processor machines.

mathStatica 2.7 Parallel Processing Engine — on Mathematica 11

mathStaticaParallelTimingsv11x

Timings in seconds using Mathematica 11 running on an R2-D2 Mac Pro computer

There is a listing of data analysis tools for MacOSX here


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9000 packages on CRAN

 

The latest update to the CRAN R archive brings the total number of packages to 9004.

Milestones:

2016-08-22: 9000 packages
2016-02-29: 8000 packages
2015-08-12: 7000 packages
2014-10-29: 6000 packages
2013-11-08: 5000 packages
2012-08-23: 4000 packages
2011-05-12: 3000 packages
2009-10-04: 2000 packages
2007-04-12: 1000 packages
2004-10-01: 500 packages
2003-04-01: 250 packages

There is a listing of data analysis tools for Mac OSX here.


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Mathematica 11 Is Now Available

 

Mathematica 11 has been released.

We are pleased to announce that Mathematica 11 has arrived, with over 500 new functions! Continuing on the path of aggressive innovation that Stephen Wolfram first embarked on 30 years ago, Version 11 embraces new areas of modern technology and introduces cutting-edge functionality to match. With Mathematica, you can now print 3D models and plots directly through either local or cloud-based 3D printers. Or instead, identify over 10,000 objects, and classify and extract features in your data with the customizable suite of enhanced machine learning tools. You can also construct, train and evaluate high-performance neural networks with both CPU and GPU support, enabling powerful deep learning in just a few lines of code. Integrated support for audio, from trimming and filters to synthesizing sounds and measuring audio, makes Mathematica 11 a flexible platform for digital audio processing and analysis.

You can read more about it in Stephen Wolfram’s blog post.


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StarDrop 6.3 released

Optibrium have just announced the release of StarDrop 6.3, perhaps the highlight of this release is the introduction of the new SeeSAR module.

The SeeSAR module developed in collaboration with BioSolve ITprovides seamless access in StarDrop to 3D structures based on X-ray crystallography or predicted with any docking software. The intuitive link between this 3D information and StarDrop’s cheminformatics analyses and visualisations, based on 2-dimensional compound structure, gives new insights into structure-activity relationships (SAR) within your project chemistry and aids the design of improved compounds. It also supports collaboration between computational and synthetic chemists, helping to share the results of 3D modelling with all decision makers.

stardrop-demo-seesar

You can watch a video tutorial here


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ICM-Scarab

 

Molsoft have just announced and interesting new product ICM-Scarab, a one-stop shop for capturing and analysing bioinformatics and chemoinformatics data. It provides and electronic notebook for storing experimental information integrated with query tools that allow the user to effortlessly search both internal and external SQL databases.

There is a webinar Wed, Jun 29, 2016 5:00 PM - 6:00 PM BST if you want to find out more.


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17th annual KDnuggets Software Data Analysis Poll

 

The results of the annual data analysis poll are in and show some interesting trends, in particular the dramatic increase in Python use.

R remains the leading tool, with 49% share (up from 46.9% in 2015), but Python usage grew faster and it almost caught up to R with 45.8% share (up from 30.3%).

Actually looking down the list I notice there is also an entry for scikit-learn, which is Python based, and if you add that in Python is now the most commonly used data analysis tool.

There was a 10% drop in the use of KNIME, and a 36% drop in the use of TIBCO Spotfire two products used in cheminformatics.

In terms of programming languages Python is by far the most extensively used.

Python 45.8% share (was 30.3%) 51% increase
Java 16.8% share (was 14.1%) 19% increase
Unix shell/awk/gawk 10.4% share (was 8.0%) 30% increase
C/C++ 7.3% share (was 9.4%) 23% decrease
Other programming languages 6.8% share (was 5.1%) 34.1% increase

In the Big Data area Hadoop (22.1%) and Spark (21.6%) dominate.

There is a listing of data analysis tools for MacOSX here.


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Cytoscape Update

 

Cytoscape has been updated to version 3.4.0

Note, This update requires Java 8 is installed and Mac OS X 10.9 and later.

Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.


Comments

Data Extractor updated

 

Data Extractor has been updated to version 1.4.2

Data Extractor allows to extract data in a sparse format contained inside various files and collect the data you need in an internal structured table. Data extractor can parse thousands and thousands of file in few seconds and collect the data inside

More details here…

There more tools for data analysis here


Comments

DB-Text

 

If you regularly have to manually edit files containing data in delimited text format then this application maybe of interest.

DB-Text is a general purpose tool for editing delimited text files. It can automatically recognise the used format analysing the content inside. It can accept data with mixed use of quotas and provides tools to copy in CSV (comma separated),TSV (tab separated) or HTML format of selected rows in the clipboard, with a simple click.

5

I've added it to the Data Analysis Tools page


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PAST, free software for scientific data analysis

 

I was just sent a link to PAST free software for scientific data analysis, with functions for data manipulation, plotting, univariate and multivariate statistics, ecological analysis, time series and spatial analysis, morphometrics and stratigraphy.

Current version (February 2016): 3.11 runs under Mac OSX 10.8 and later.

Hammer, Ø., Harper, D.A.T., Ryan, P.D. 2001. PAST: Paleontological statistics software package for education and data analysis. Palaeontologia Electronica 4(1): 9pp. http://palaeo-electronica.org/20011/past/issue101.htm

I've added it to the page of data analysis packages for Mac OSX.


Comments

Shinobicontrols iOS charting

 

I've just been sent a link to an advanced charting kit for mobile devices Shinobicontrols if you are developing an iOS app that requires plots or charts this may be a useful addition.

If you are looking for a graphing toolkit for both iOS and MacOS then it might be worth looking at the tools from VVI


Comments

Tabula is awesome!

 

I recently needed to download the supplementary information provided with a publication, my heart sank when I saw it was provided as a PDF file. My worst fears were justified when I tried to simply copy and paste SMILES strings together with 5 columns of data into a spreadsheet, no chance of it copying across in an ordered manner!

Then I tried Tabula a tool for "liberating data tables locked inside PDF files". It worked perfectly, nearly 2000 rows of data spread over 11 pages converted to a csv file in a couple of mouse clicks. This is wonderful and should be part of any data scientists toolkit.

It is included on the Data Analysis Tools page but really deserves a special mention.


Comments

RRegrs: an R package for computer-aided model selection with multiple regression models

 

I just thought I'd flag a paper in Journal of Cheminformatics, RRegrs: an R package for computer-aided model selection with multiple regression models DOI.

We propose an integrated framework for creating multiple regression models, called RRegrs. The tool offers the option of ten simple and complex regression methods combined with repeated 10-fold and leave-one-out cross-validation. Methods include Multiple Linear regression, Generalized Linear Model with Stepwise Feature Selection, Partial Least Squares regression, Lasso regression, and Support Vector Machines Recursive Feature Elimination. The new framework is an automated fully validated procedure which produces standardized reports to quickly oversee the impact of choices in modelling algorithms and assess the model and cross-validation results. The methodology was implemented as an open source R package, available at https://www.github.com/enanomapper/RRegrs, by reusing and extending on the caret package.

Comments

Wizard Pro updated

 

Wizard Pro has been updated.

What's New in Version 1.7.18

  • Added support for Numbers 3.6 files
  • Exporting data from the Summary view now has a progress bar and cancel button
  • Exporting data now writes directly to disk instead of building the file in memory first
  • Many other performance improvements throughout the program
  • Added support for generating the R command for the Friedman test
  • Added support for generating SAS/SPSS commands for repeated-measures tests
  • Report the combined significance of constant coefficients for models with multiple sets of coefficients
  • Fix a crash after exporting ROC curves
  • Fix a bug when exporting DTA files with missing values
  • Fix a bug where formatting options weren't showing in the Pivot view
  • Fix a number of minor interface glitches
  • Improved support for importing SAS and SPSS command files
  • Improved support for SAS catalog files

There is a review of Wizard Pro here, and a listing of data analysis tools for Mac OSX here.

Comments

Data Creator Updated

 

Data Creator has been updated. This is an invaluable tool if you ever need to create a pseudo-random data-set.

What's New in Version 1.5 • New creator type: USA cities, Italian cities, French cities, German Cities. • Bug fix: Changing format to export, the file extension was not changing automatically • Other minor bug fix. • Optimized for OS X 10.11 El Capitan

Data Creator can create sample tables (rows and columns) as you like and fill them with pseudo-random proper content (rows of content) with a single click. You can select which kind of fields (columns) you like (name of animals, colors, fruits, english surname, german names and so on with over 50 different kind of data) and have all the contents filled for how many rows you like in a click.

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Wizard Pro updated

 

The popular data analysis tool Wizard Pro for Mac has been updated. Wizard includes a full set of tools for doing professional research, yet its friendly interface makes statistics accessible to beginners. There is a review here.

New in 1.7.17:

• Show ellipses when data is truncated in the Raw Data view
• Fix a bug where Shapiro-Wilk and one-column Kolmogorov-Smirnov tests on highly repetitious data gave overly conservative results
• Improved support for exporting Stata .dta files
• Improved support for importing compressed SAS data files
• Improved support for importing SAS catalog files containing a large number of value labels

There is a comprehensive listing of data analysis tools for MacOSX here.

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Computational chemistry guides & tools

 

The Medicines for Malaria Venture have an interesting page in which they are accumulating a list of computational tools and guides describing the use of the tools to address key issues within the drug discovery process.

Tools were chosen to address common needs expressed by medicinal and computational chemists working in the not-for-profit area. Recognising that this is a global effort, we have selected software packages on the basis of being free for all users.

The guides are either text descriptions or webcasts showing the tool in action. To date they include DataWarrior, KNIME, YASARA, ChEMBL and PK Tool.

Comments

csvkit

 

csvkit is a suite of utilities written in Python for converting to and working with files in csv format. csvkit is designed to be used a replacement for most of Python’s csv module simply

import csvkit

It can also be called from the command line

in2csv data.json > data.csv

To install on a Mac you can use use PIP a tool for installing and managing Python packages.

pip install csvkit

It is supported on OSX and Linux. It also works–but is tested less frequently–on Windows.

Comments

pro Fit 7 released

 

pro Fit has been updated to version 7, it is a Mac OS X application for data/function analysis, plotting, and curve fitting. This is a complete rebuilding of pro Fit from the ground up to complete the transition to cocoa and the latest Mac OS X technologies.

The release notes give full details but a couple of notable features are

  • 64 bit architecture: pro Fit comes as a universal binary and runs in 64 bit mode by default. If you need to run pro Fit under 32 bit (e.g. because you want to link to a 32 bit plug-in or Python module), you can set it to run under 32 bit mode by choosing Get Info in the Finder.
  • Global search: It is now possible to search for a text string simultaneously in all text, data, and drawing windows.
  • Sandboxing: pro Fit 7 is a sandboxed application, supporting all standard security features offered by the OS. As a side effect, the location of the plug-in folder has changed. To locate it, choose "Open user's plug-in folder" from the "Customize" menu.
  • Scripting: pro Fit 7 changed the interfaces to some commands, which sometimes required that some of the programming interfaces be modified, too. In addition, we harmonized some naming conventions in our programming interfaces. Please see the "programming" read me file for more details.
  • The fitting engine now can (optionally) use long-double precision for enhanced accuracy.
  • pro Fit now supports high-resolution images on retina displays.

Sandboxing does of course mean a few changes.

pro Fit cannot access files outside its application container without explicit user permission. The application container is found under "~/Library/Containers/com.quansoft.profit". Therefore:

If you are running a script that accesses files outside pro Fit's containers, e.g. in your Documents folder, you must grant pro Fit explicit permission to do so: Choose Preferences form the pro Fit menu, and navigate to the tab Security. Then, add the desired directory to the list of accessible directories. The permission will be permanently stored, i.e. it will persist even if you restart pro Fit.

The "pro Fit plug-ins" folder, which contains scripts and plug-ins to be automatically loaded during start-up, is now placed in pro Fit's container (under ~/Library/Containers/com.quansoft.profit/Data/Library/Application Support/com.quansoft.profit/pro Fit plug-ins). To navigate to that folder, choose "Open User's Plug-in folder" from the cutomize menu.

There is a list of data analysis tools for Mac OS X here.

Comments

Wizard Pro Updated

 

The popular data analysis and plotting application has been updated New in 1.7.9:

• Fix a crash when opening a document with a Quantile column
• Fix a crash when attempting to use a column as its own join key
• Fix an occasional crash after entering or leaving Full Screen mode
• Fix a few minor interface glitches
• Bug fix: the XLS and JSON exporters did not properly respect Data Filters
• Bug fix: Time-of-day columns derived from other columns were not properly displayed in the Raw Data view
• Bug fix: weighted log-linear models sometimes produced an error
• Bug fix: a model's constant term was not included when exporting the coefficient table as XLS
• Feature: Include prediction intervals when exporting prediction tables

There is a review of Wizard Pro here.

Comments

Tabula 1.0 released

 

If you have ever been in the situation where supporting information for a publication is provided in PDF format then you will appreciate Tabula. Tabula allows you to extract that data into a CSV or Microsoft Excel spreadsheet using a simple, easy-to-use interface.

I've added it to the page of data analysis tools.

Comments

Poll on data analysis tools

 

The results of the 16th annual KDnuggets Software Poll on data analysis tools is in.

The top 10 tools by share of users were

R, 46.9% share ( 38.5% in 2014, 37% in 2013)
RapidMiner, 31.5% ( 44.2% in 2014, 39% in 2013)
SQL, 30.9% ( 25.3% in 2014, NA in 2013)
Python, 30.3% ( 19.5% in 2014, 13% in 2013)
Excel, 22.9% ( 25.8% in 2014, 28% in 2013)
KNIME, 20.0% ( 15.0% in 2014, 6% in 2013)
Hadoop, 18.4% ( 12.7% in 2014, 9% in 2013)
Tableau, 12.4% ( 9.1% in 2014, NA 2013)
SAS, 11.3 (10.9% in 2014, 10.7% in 2013)
Spark, 11.3% ( 2.6% in 2014, NA in 2013)

The results very much reflect my own interactions, whilst R has a significant installed user base and of course a vast repository of open source packages, Python seems to be gaining traction. Certainly in part because Python seems to have become the lingua franca for scientific computing.

I've always thought of KNIME and Tableau as excellent tools for implementing workflows but looking at recent iterations it is clear there is now greater emphasis on interactive analysis.

There is a listing of data analysis tools for Mac OS X here.

Comments

CheS-Mapper Updated

 

CheS-Mapper has been updated. CheS-Mapper (Chemical Space Mapper) is a 3D-viewer for chemical datasets with small compounds. Whilst executable jar files can be downloaded from the website the source code is available on GitHub.

There is a review of an older version of Ches-Mapper here.

Comments

SpeckTackle

 

The latest issue of Journal of Cheminformatics has a paper that might be of interest to a variety of people involved in spectroscopy or data visualsation. SpeckTackle: JavaScript charts for spectroscopy.

We present SpeckTackle, a custom-tailored JavaScript charting library for spectroscopy in life sciences. SpeckTackle is cross-browser compatible and easy to integrate into existing resources, as we demonstrate for the MetaboLights database. Its default chart types cover common visualisation tasks following the de facto ‘look and feel’ standards for spectra visualisation.

SpeckTackle is an open-source JavaScript library to create custom-tailored charts for spectroscopy in life sciences. Implemented charts exist for mass spectrometry, one- and two-dimensional NMR, UV/VIS, IR, and general continuous data use cases such as chromatograms.

The authors kindly supply a demo web page demonstrating different chart types and functions of the SpeckTackle library. Example data is embedded in the web page (800 kb file size). Click on the buttons at the top of the page to see the data displayed. For the Chromatogram, Difference Chart and Spectral Match click the button then the Add Data button.

Highlighting a section of the spectra expands the view and mouseover on the 2D NMR spectra provides a tooltip giving chemical shifts

I've added this to the spectroscopy resources page

Comments

DataWarrior Update

 

DataWarrior 4.1.1 is available for download, in addition to precompiled binaries all Java source files and the script to build DataWarrior on Linux/MacOSX can be downloaded for free use under the GNU public license. DataWarrior is a free data visualization and analysis program with embedded chemical intelligence.

datawarrior2

There is a review of DataWarrior here.

Comments

Wizard Pro 1.7.4

 

The popular data analysis tool Wizard Pro has been updated to version 1.7.4.

New in 1.7.4:

  • Fix a display issue in the Summary view when unchecking filters
  • Fix a crash in the Predict view when a model has either no outcome variables or no explanatory variables
  • Fix "Can't connect" error when attempting to connect to a database using a password containing special characters
  • Support for connecting to databases over IPv6
  • Support for schemas in PostgreSQL
  • Support for character types in PostgreSQL
  • Improved support for importing CSV files with improperly quoted values
  • Improved support for importing variable labels and frequency weights from SPSS files
  • Increased maximum length of exported SPSS variable labels from 120 characters to 256 characters

There is a review of Wizard Pro here, and there is a listing of data analysis tools for Mac OS X here.

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Scripting Vortex 25

 

Whilst most of the Vortex scripts mentioned on this site to date involve chemical structures we should not forget that Vortex is an excellent general data analytics tool and the data set does not have to include any molecular structures. Recently I was asked about the number of publications associated with a particular potential therapeutic target and it struck me that Vortex might actually be an excellent tool to investigate this.

Read More.

vorte25_1

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A review of Wizard Pro

 

When I first started the list of data analysis packages for Mac OS X it was a fairly short list, over the years the list has grown and the diversity of packages increased. From free packages like R to enterprise applications like IBM SPSS costing thousands. Some packages are enormously powerful but have a ferocious learning curve, whilst others are very easy to use but have only very limited capabilities. Wizard is an intuitive data analysis tool, designed from the ground up to be readily accessible but still retain the power of the sophisticated command line driven applications that only seem suitable for programmers. Wizard Pro allows the user to explore the data interactively without the need to learn a programming language. Read more here.

Update

I should have added Wizard Pro runs under Yosemite and is on the list of Yosemite compatible applications, and has just been updated to version 1.6.7 (Feb 27th).

Comments

MOSAIC is a modular toolbox for analyzing data from single molecule experiments

 

The interactions of single molecules with nanopores are observed by measuring changes to the ionic current that occurs when the pore changes from an unoccupied (i.e., an open channel) to an occupied state. The electrical nature of the measurement allows us to model components of the physical system with equivalent electrical elements, and describe system behaviour collectively with the circuit response.

MOSAIC is a modular toolbox for analyzing data from single molecule experiments. Primarily developed to analyze data from nanopore experiments. MOSAIC’s GUI greatly simplifies analyzing data from single-molecule nanopore experiments and provides easy access to most common algorithms and data types. MOSAIC can also be scripted using PYTHON to run multiple analyses in batch mode. It can also be integrated into Mathematica, MATLAB or IGOR Pro workflows.

Balijepalli, A. Ettedgui, J, Cornio, A. T., Robertson, J. W. F. Cheung, K. P., Kasianowicz, J. J. & Vaz, C., ACS Nano 2014, 8, 1547–1553

Comments

Datamate Numeric Processor

 

Datamate Numeric Processor allows you to Normalize, standardize, scale, and manage missing data and data outliers quickly and accurately.

There is a listing of data analysis tools for Mac OS X here.

Comments

Data Extractor has been updated

 

Data Extractor has been updated to version 1.4. Data Extractor allows to extract data in a sparse format contained inside various files and collect the data you need in an internal structured table. Collected data can be exported at any time in various format (CSV, TSV, HTML, Custom). Data extractor can parse thousands and thousands of file in few seconds and collect the data inside. It uses simple smart instructions about how to recognize the data you need, how to extract them and where to put these data inside a structured table, ready to be exported.

Update includes

  • Usage of prefix to identify a data with data on a newline (prefix with newline at end)
  • More resilient extraction algorithm
  • Faster algorithm, often 10x time faster of the previous release
  • Improved multithreading capabilities
  • Fast adding of DataBase fields during 'Extraction Rules' editing and adding
  • Extraction of data based on position (example: 3th element of a tab separated values row) at popular demand
  • Solved a bug causing crash during extractions under certain circumstances
  • Solved a bug with double newline at the end of files
  • Solved a bug under other specific text characteristic of files to extract
  • Other generic bug fixes

There are more data analysis tools here

Comments

Alternative to OriginLab for Mac

 

A reader has contacted me asking for suggestions for alternatives to OriginLab that run on a Mac. Whilst you can run OriginLab under virtualisation there are many Data Analysis Packages that run under Mac OS X natively but I don't know enough about OriginLab to suggest which has similar capabilities. Any suggestions?

Comments

Data Creator updated

 

Data Creator has been updated to version 1.4.

Data Creator is an advanced data generator that can create table filled with pseudo-random custom content in just few clicks, absolutely invaluable when you need data to test a database of data analysis tool.

What's New in Version 1.4

  • New (faster) algorithm for records creation
  • Better handling of creation of a higher number of records in a single command
  • Improved more informative progress toolbar for longer operations
  • More commands to add, delete and set number of records
  • Improved menus
  • Bug fix regarding the fields table
  • Bug fix regarding the record table
  • Other bug fixes
  • Improved general stability using a more resilient code

There is a review of Data Creator here.

Comments

Plot2 a scientific 2D plotting program

 

I've just added Plot2 to the list of data analysis tools available for Mac OS X.

This project started in 1993 with SciPlot on NeXTStep and was updated at the end of November 2014. Plot2 is designed for everyday plotting, it is easy to use, it creates high quality plots, and it allows easy and powerful manipulations and calculations of data.

Comments

VIDA v4.3.0 released

 

OpenEye have announced the release of VIDA v4.3. This is a major update with many new features and enhancements, including improvements to depiction, 2D alignment, list manager manipulation, surface selection and display, default colouring schemes, both visual and list-driven atom subset selection, cluster viewing, colouring by SD property and extension management.

One feature I’m sure will be very popular is the new advanced depiction options, including atom property maps from the Grapheme TK, substructure highlighting, and 2D structure alignment, are available for depiction in the 2D window and spreadsheet

2Ddisplay

Support for Mac OS X 10.8 and 10.9 was added
Mac OS X 10.6 is no longer supported


Comments

ConTour: Data-Driven Exploration of Multi-Relational Datasets for Drug Discovery

 

Caleydo is an open source visual analysis framework targeted at biomolecular data. It has been described in a number of publications and I noticed that a recent project ConTour included chemical structures.

Large scale data analysis is nowadays a crucial part of drug discovery. Biologists and chemists need to quickly explore and evaluate potentially effective yet safe compounds based on many datasets that are in relationship with each other. However, there is a is a lack of tools that support them in these processes. To remedy this, we developed ConTour, an interactive visual analytics technique that enables the exploration of these complex, multi-relational datasets.

Christian Partl, Alexander Lex, Marc Streit, Hendrik Strobelt, Anne-Mai Wassermann, Hanspeter Pfister, Dieter Schmalstieg ConTour: Data-Driven Exploration of Multi-Relational Datasets for Drug Discovery IEEE Transactions on Visualization and Computer Graphics (VAST '14), to appear, 2014.

I’ve added Caleydo to the listing of data analysis tools.

Comments

Chemistry document classifier

 

The latest issue of J Cheminformatics has an article entitled “A document classifier for medicinal chemistry publications trained on the ChEMBL corpus”, Journal of Cheminformatics 2014, 6:40 doi:.

The large increase in the number of scientific publications has fuelled a need for semi- and fully automated text mining approaches in order to assist in the triage process, both for individual scientists and also for larger-scale data extraction and curation into public databases. Here, we introduce a document classifier, which is able to successfully distinguish between publications that are ‘ChEMBL-like’ (i.e. related to small molecule drug discovery and likely to contain quantitative bioactivity data) and those that are not. The unprecedented size of the medicinal chemistry literature collection, coupled with the advantage of manual curation and mapping to chemistry and biology make the ChEMBL corpus a unique resource for text mining.

The models, workflows and tools are freely available for download. https://github.com/chembl/chemblliteratureclassifier

Comments

CheS-Mapper updated

 

CheS-Mapper has been updated to version 2.4.

New Features Add Moss as new structural fragment mining algorithm Show the number of distinct 3D positions (at the top right, alongside other dataset info) Mapping warnings are now acessible within the viewer (Menu: Help > Show mapping warnings) Add hint for multiselection of compounds via 'control'-key (is shown when zooming into compounds for the first 3 times) More Changes The viewer no longer zooms out when changing component size or spread Add log conversion of feature values, by adding a new feature, instead of log-highlighting (gives better overview of log-distributed values, e.g. within the chart) Multiple selected compounds are now highlighted within the chart for nominal features (was only possible for numerical features) Fix Fix error that showed strucutural fragment values as '1'/'0' instead of 'match'/'no-match'

CheS-Mapper (Chemical Space Mapper) is a open source 3D-viewer for chemical datasets of small molecules, a publication in the Journal of Chemiformatics describes an early version of the application DOI: 10.1186/1758-2946-4-7, and there is a review here.

Comments

Sage mathematics software

 

Sage is a Python based free open-source mathematics software system licensed under the GPL. It builds on top of nearly 100 open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R to provide a common unified interface, either as a notebook in a web browser or the command line.

In addition to a local installation it is also possible to use SageMathCloud a free service with support from the University of Washington.

I’ve added Sage to the list of data analysis tools for Mac OS X.

Comments

CheS-Mapper 2.2 released

 

CheS-Mapper has been updated, CheS-Mapper (Chemical Space Mapper) is a 3D-viewer for chemical datasets with small compounds.

The tool can be used to analyze the relationship between the structure of chemical compounds, their physico-chemical properties, and biological or toxic effects. CheS-Mapper embedds a dataset into 3D space, such that compounds that have similar feature values are close to each other. It can compute a range of descriptors and supports clustering and 3D alignment.

There is a review of Ches-Mapper here

Comments

R version 3.1.1 released.

 

I just noticed that R was updated last month to version 3.1.1 ((Sock it to Me).

R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms.

I’ve also updated the list of Data Analysis packages for Mac OSX.

Comments

Sentira Review

 

Sentira is a new chemical data visualisation tool from Optibrium. The focus is on ease of use data visualisation and as such is probably targeted at the bench scientist rather than a specialist computational scientist. It supports a selection of plotting and SAR tools.

I’ve written a review of my first impressions.

There is also a list of data visualisation applications here.

Comments

Datawarrior review

 

DataWarrior is a data analysis tool that understands chemistry, it provides an efficient way to search, sort and analyse structure-activity data. DataWarrior was developed at Actelion and it is highly integrated into the drug discovery platform, in 2014 it was decided to release DataWarrior without the integration layer as a stand-alone tool to the public. DataWarrior is a Java application and thus is cross platform.

I’ve written a review on my initial impressions.


Comments

Aabel NG released

 

Gigawiz have just announced the release of an updated version of Aabel.

Aabel™ NG is the result of a 5-year special project and massive development effort, rewriting millions lines of code to transform the Gigawiz flagship product into an icon of power and simplicity for professional users.

The update includes:

  • Modernization and optimization of the main processing code
  • A total redesign of the user interface, adding power with modeless simplicity
  • Complete Carbon (32-bit)-to-Cocoa (64-bit) transformation
  • Minimizing overhead between the user interface and the main processing code (a crucial step for sustainability and future development)
  • Replacement of high-level Cocoa classes with Aabel NG-specific code, a key alteration for any part of the application that requires high performance with large data sets
  • Addition of numerous new features

The transformation to 64-bit should enable much larger data sets to be handled, and there are a host of new statistical methods however I’m not familiar enough with the area to comment on how useful they are.

Interactive graphing means that you no longer have to manually update a plot to see how the changes look, the enhanced exploratory analytics could be really useful when working with large data-sets.

A Mac OS X Mavericks; Intel- based Mac and a colour monitor with a minimum resolution of 1440 x 900 is required. There are also a couple of issues with backward compatibility.

Aabel v3/v2 are 32-bit applications; Aabel NG (v4) is 64-bit and hence cannot use Apple data structures and formats that have not been ported to 64-bit. In summary, the implications are as follows: A feature of Aabel v3/v2, called database metaphor (i.e., a container that refers to a collection of worksheets), due to its dependency on Apple 32-bit subsystems, is not available in the 64-bit version. While Aabel NG (v4) reads the worksheet files of Aabel v3/v2, it will NOT be able to read their viewer files, because the latter files have contents that require Apple 32-bit subsystems (which are unavailable in 64-bit). In Aabel v3/v2, the System Alias Manager manages the connections between the graphs and their source worksheets. The Alias Manager has unresolved issues making the continuation of its use not sustainable. In Aabel NG (v4), the saved graphs will be hot-linked to their source worksheets along paths defined at the time their pipelines are created.

The price of the new version is $1250 (academic $750) and there are reduced pricing for upgrades.

I’m using Aabel 3 at the moment and I’m very happy with it, I’d be very interested to hear from anyone who upgrades.

Comments

DataDesk 7 released

 

I’m delighted to report DataDesk 7 has been released, this update requires a Macintosh computer running Mac OS X 10.6, 10.7, 10.8, or 10.9 and Intel processor and 2 GB RAM.

Data Desk brings fast, easy-to-use visual analysis to your desktop. It provides interactive graphical tools for exploring and understanding your data—for finding the patterns, relationships, and exceptions. While it implements many traditional statistics techniques suitable for data from planned experiments and sample surveys, Data Desk’s true strength is its powerful tools for data exploration. Its insightful graphic displays simplify intuitive investigation of your data.

DataDesk can handle very large datasets (up to 2 billion cases), it supports a wide variety of statistical techniques and supports linked plots so that selections in one plot are highlighted in another so you get multiple views of your data. They have supported the Mac since the mid 1980’s and I suspect it is now the oldest commercial application for the Mac. A series of continuous updates have kept DataDesk at the forefront of data analysis. The accompanying manual also serves as an invaluable resource for learning statistical analysis.

I’ve updated the list of data analysis tools available for the Mac.

Comments

Scripting Vortex 21, displayling web pages

 

Well things can change quickly at times, in the last tutorial I wrote..

Vortex has a limited capacity to render HTML, it is however a very limited ability so there is no support for javascript or CSS but you can introduce a number of useful extra features.

If you download the latest daily build of Vortex from the Dotmatics Support site there is a version that comes bundles with Java 8, if you download this version are a host of new options for displaying plots. In particular you can now display web pages, follow links on pages, and there is support for javascript.

In Scripting Vortex 21 there is a demonstration of this feature and an example script that uses SMARTCyp to predict sites of metabolism.

plotDemo3

There are many more scripts on the Hints and Tutorials Page.

Comments

Scripting Vortex 20

 

Vortex has a limited capacity to render HTML, it is however a very limited ability so there is no support for javascript or CSS but you can introduce a number of useful extra features.

Im the latest tutorial you can find out how to use this to add images, plots and graphs to the molecular worksheet.

Scripting Vortex 20:-Adding images to Vortex

radarplots

Comments

Panoply netCDF, HDF and GRIB Data Viewer

 

I’ve just added Panoply to the list of data analysis applications. Panoply is an application from NASA that plots geo-gridded and other arrays from netCDF, HDF, GRIB, and other datasets. You can:-

  • Slice and plot geo-gridded latitude-longitude, latitude-vertical, longitude-vertical, or time-latitude arrays from larger multidimensional variables.
  • Slice and plot "generic" 2D arrays from larger multidimensional variables.
  • Slice 1D arrays from larger multidimensional variables and create line plots.
  • Combine two geo-gridded arrays in one plot by differencing, summing or averaging.
  • Plot lon-lat data on a global or regional map using any of over 100 map projections or make a zonal average line plot.
  • Overlay continent outlines or masks on lon-lat map plots.
  • Use any of numerous color tables for the scale colorbar, or apply your own custom ACT, CPT, or RGB color table.
  • Save plots to disk GIF, JPEG, PNG or TIFF bitmap images or as PDF or PostScript graphics files.
  • Export lon-lat map plots in KMZ format.
  • Export animations as AVI or MOV video or as a collection of individual frame images.
  • Explore remote THREDDS and OpenDAP catalogs and open datasets served from them.

panoply

Comments

The Data analysis app Wizard Pro has been updated

 

Wizard Pro has just been updated. Wizard Pro is a data analysis application with easy exploration in mind. The new release notes include

FEATURES

  • Database support: import from SQLite, MS Access, MySQL, and PostgreSQL
  • Numbers '13 support
  • Timestamp / time-of-day support
  • Customizable data partitions. Separate numeric data into groups of equal size, intervals of equal width, or user-defined intervals
  • Best-fit lines on scatterplots, and reference lines on Q-Q plots
  • Visualize critical values and p-values with the new Bottom Line popover (see screenshots)
  • New "Copy Predicted Values" menu item applies a predictive model to the full data set

CHANGES

  • Histograms are much sharper now
  • More tick marks and labels on all the graphics
  • Full access to the Column tools from inside the Raw Data view
  • New preference option: choose a "Friendly" or "Neutral" font for The Bottom Line
  • Filtered and frequency-weighted models run much faster than before
  • Excel output is much prettier -- with bold, italics, and indentation for clarity.

NICE TOUCHES

  • Exporting data now has a progress bar and a Cancel button
  • Support for up to 6 data filters
  • Support for up to 5 pivot columns

There are more graphing or plotting applications on the data analysis page.

Comments

DataGraph updated to version 3.2

 

I just saw that the highly regarded DataGraph has been updated, this update includes:

  • Pivot Table command - great for data analysis.
  • Hover information to inspect data in a plot.
  • A new method to import text files.
  • Runs faster when you have large data sets.
  • Improvements to basically every drawing command.
  • More formatting options.
  • More operations to edit data, automatically fill in entries etc using menu and context menu entries.
  • Can label graphs and export multiple graphs at the same time

There are more graphing or plotting applications on the data analysis page.

There is a review of DataGraph 3.0 in The Journal of Statistical Software

Comments

KST added to list of data analysis tools

 

I’ve just added KST to the list of data analysis applications for Mac OSX

Features of Kst include:

  • Robust plotting of live "streaming" data.
  • Powerful keyboard and mouse plot manipulation.
  • Powerful plugins and extensions support.
  • Large selection of built-in plotting and data manipulation functions, such as histograms, equations, and power spectra.
  • A number of unique tools which dramatically improve efficiency, such as the "Data Wizard" for fast and easy data import, the "Edit Multiple" mode to bulk-edit most objects, or the "Change Data File" tool to compare results from different experiments
  • Color mapping and contour mapping capabilities for three-dimensional data, as well as matrix and image support.
  • Monitoring of events and notifications support.
  • Built-in filtering and curve fitting capabilities.
  • Convenient command-line interface.
  • Powerful graphical user interface with non-modal dialogs for an optimized workflow.
  • Support for several popular data formats.
  • Multiple tabs.
  • Extended annotation objects similar to vector graphics applications.
  • High-quality export to bitmap or vector formats.

Comments

Graph Builder Updated

 

Graph Builder has been updated to version 10.9.16.

  • Made the heat map (aka: image map, point fill) and 3D scatter, surface and volume color mapping editor significantly better.
  • Added a palette that shows how to script a multi-level animated pie chart.
  • Removed depreciated system calls.
  • Adjusted many items under the hood in preparation for v11.
  • Special Note: The v11 build is being worked on and your feedback to support@vvi.com is very welcome.

Graph Builder is a powerful application rich in graphic editing, creation and programming to facilitate the visualization of information. It has a good complement of 2D and 3D graph features, a full-fledged user interface and is programmable. Paste data into table editors, write scripts to generate data, load a Xcode plugin you write for data generation and to retrieve data from external sources.

There is a comprehensive list of data analysis tools for Mac OSX here.

Comments

GAUSS Mathematical and Statistical System

 

I’ve just added GAUSS Mathematical and Statistical System to the page of data analysis tools for Mac OS X.

The GAUSS Mathematical and Statistical System is a fast matrix programming language widely used by scientists, engineers, statisticians, biometricians, econometricians, and financial analysts. Designed for computationally intensive tasks, the GAUSS system is ideally suited for the researcher who does not have the time required to develop programs in C/C++ or FORTRAN but finds that most statistical or mathematical “packages” are not flexible or powerful enough to perform complicated analysis or to work on large problems.

Comments

Data analysis tools

 

I’ve just updated the Data Analysis tools for Mac OSX page. I’ve fixed the broken links and added another eight packages to bring to total upto ninety. Browsing through it looks like just about every area of science is covered, from open-source packages to enterprise focussed applications.

Comments

Graph-R

 

I’ve just added Graph-R to the page of data analysis tools.

Graph-R is an application used to create 3-dimensional contours, contour lines, wire frames, and scatter diagrams from numeric data files(CSV files). Graph setting is easy. The perspective direction can be freely changed using your mouse. Graph that are created can be saved as PNG or JPEG files.

This software requires Mac OSX 10.8 or later.

Comments

Graph Builder

 

I just got a message about an update to Graph Builder a very popular and powerful application from VVimaging, Inc rich in graphic editing, creation and programming to facilitate the visualization of information. It has a excellent complement of 2D and 3D graph features, a full-fledged user interface and is programmable. Paste data into table editors, write scripts to generate data, load a Xcode plugin you write for data generation and to retrieve data from external sources. Also supports dynamic graphs.


Comments

Regress+2.7.1

 

The free univariate data modeling package Regress+ has been updated to version 2.7.1.

Regress+ offers:-

  • Plain textfile input
    • Equations, with or without uncertainties (weights)
    • Distributions, continuous or discrete data
    • Discrete data grouped or ungrouped
  • Datasets up to 4,294,967,295 points (minimum 7)
  • Up to 10 parameters
  • User-selected optimization criterion (where appropriate)
    • Least squares
    • Minimum average abs(residual)
    • Maximum likelihood
    • Minimum K-S statistic
    • Minimum chi-square statistic
  • Full, dated Report (textfile)
  • Robust goodness-of-fit testing for distributions
    • Tunable precision
  • [Optional] State-of-the-art (BCa) central confidence intervals (90, 95 and 99 percent)
    • Tunable precision
  • High-quality (PDF, PNG) plots with one keystroke!
    • X/Y plot, with or without error bars
    • PDF plot
    • CDF plot
    • Probability plot for goodness-of-fit (see above)
    • [Optional] Logarithmic axes (when appropriate)
    • Editable axis labels
    • Automatic tick marks/labels (see above)
  • [Optional] Predictions for unobserved values or percentiles
    • With confidence intervals if desired
  • [Optional] Constant parameter(s)
  • 21 Built-in Equations
    • Plus user-defined model
    • [Optional] Test residuals for systematic error
    • [Optional] List data with fitted estimates and residuals
    • [Optional] Simulated-annealing mode for initial parameter estimates
  • 59 Built-in Distributions
    • 9 continuous, symmetric
    • 27 continuous, skewed
    • 11 continuous mixtures
    • 6 discrete
    • 6 discrete mixtures
    • [Optional] Creation of synthetic samples
  • No hidden assumptions anywhere
    • No approximations, apart from those common to sampling and bootstrapping generally
    • No data transformations of any kind
  • Extensive documentation

There is comprehensive listing of Mac OSX data analysis packages here.

Comments

R update

 

I just noticed that there is an update to R on the CRAN website

This binary distribution of R and the GUI supports 64-bit Intel based Macs on Mac OS X 10.6 (Leopard) or higher. Since R 3.0.0 the binary is a single-arch build and contains only the x86_64 (64-bit Intel) architecture. PowerPC Macs and 32-bit Macs are only supported by building from sources or by older binary R versions. The default package type is "mac.binary" and the binary repository layout has changed accordingly.

There is a listing of data analysis packages for Mac OS X here.

Comments

Scripting Vortex 16

 

OCHEM is a free open access site of annotated models and chemical data. OCHEM contains 1831772 experimental records for about 477 properties collected from 12457 sources you are free to upload your own data and also build predictive models using existing or your own data.

There are also a number of already built models that the public can access, these include

  • Ames test
  • CYP1A2 inhibition
  • LogP and Solubility

You can run predictions on OCHEM using simple REST-like web services, these vortex scripts submit tasks to the various models and then retrieve the resulting prediction.

Comments

Graph Builder updated

 

Graph Builder has been updated

  • Added data input for 2D vector field presentation.
  • Added programmed and animated 2D vector field palette.
  • Updated script documentation for 2D vector field animation and programming.
  • Added a preference option to turn on the built-in network graphing server.
  • Added ability to display dynamic and programmed Graph Builder document results over the web.
  • Updated the manual to explain new features

There is a listing of data analysis applications for Mac OSX here.

Comments

Updated Applescript Resources

 

I’ve just updated the Applescript Resources page, in particular I’ve included updates to the great tools provided by Satimage-Software. These include Smile a programming and working environment that you can use in a variety of situations. You may want to perform a scientific work, to handle cgi requests, to automate an intensive file processing task, to produce computed graphics, to edit XML files, to work with Unicode texts, to make GUI of your scripts, and SmileLab the SmileLab license adds the data visualization features to Smile, the automation environment by Satimage-Software.

smilelabhome

In SmileLab you can

  • extract data from files (default data formats supported: text, binary, FITS, XNF, ...),
  • perform data processing using commands provided with Smile or controlling external code
  • visualize your data in the most usual forms (curves, scatter plots, bar graphs, contour lines, color maps and vector fields in 2D, and 3D surfaces),
  • customize the interaction of the user with the plots (handling mouse clicks, contextual menus, keyboard events...) and create custom interfaces,
  • export your plot as a PDF file, as a bitmap picture (PNG, JPEG, TIFF, BMP, PSD) or as a QuickTime movie.


Comments

StarDrop 5.4

StarDrop was recently updated to version 5.4, this brings an update to the virtual library design module and scaffold based design, there have also been improvements to the plotting and data visualisation.

There are now seven optional plugins with three exciting new options.

Derek Nexus™ - Knowledge based toxicity prediction The new Derek Nexus module for StarDrop provides Lhasa Limited's world-leading technology for knowledge-based prediction of key toxicities. Using data from published and donated (unpublished) sources, Derek Nexus identifies structure-toxicity relationships that alert you to the potential for your compounds to cause toxicity. The Derek Nexus module provides predictions of the likelihood of a compound causing toxicity in over 40 endpoints, including mutagenicity, hepatotoxicity and cardiotoxicity.

BIOSTER™ - A world of chemistry experience BIOSTER is developed and updated in collaboration with Digital Chemistry and is available as an optional extension to StarDrop's Nova module. This combination enables you to quickly and easily search the comprehensive BIOSTER database to identify transformations that are relevant to your compounds. These can be automatically applied to generate novel structures with a high likelihood of biological activity and synthetic accessibility, prioritised against the property profile you require for your project. BIOSTER brings the collective experience of the chemistry community to help you to discover new active analogues of your compounds based on the tried and tested principle of isosterism. The BIOSTER module contains a unique compilation of over 20,000 precedented bioisosteric transformations, manually curated from the literature by Dr István Ujváry, complete with references to the original publications in which they are described.

torch3D™ The renamed torch3D module, using Cresset’s unique Field technology to understand and apply 3D Structure Activity Relationship (SAR), has been updated to include the latest version of Cresset’s XED force field providing insight into compounds’ 3D structures, biological activities and interactions.

These certainly significantly expand the potential utility of StarDrop, but note that these are not part of the standard install and may require additional licensing.



Comments

fmcsR: Mismatch Tolerant Maximum Common Substructure Searching in R

I’m not a big user of R a free software environment for statistical computing and graphics, but occasionally I notice cheminformatics modules being published. The latest issue of Bioinformatics DOI has a paper describing “fmcsR: Mismatch Tolerant Maximum Common Substructure Searching in R”.

The fmcsR package provides an R interface, with the time consuming steps of the FMCS algorithm implemented in C++. It includes utilities for pairwise compound comparisons, structure similarity searching, clustering and visualization of MCSs. In comparison to an existing MCS tool, fmcsR shows better time performance over a wide range of compound sizes. When mismatching of atoms or bonds is turned on, the compute times increase as expected, and the resulting FMCSs are often R1C5 substantially larger than their strict MCS counterparts. Based on R1C6 extensive virtual screening (VS) tests, the flexible matching feature enhances the enrichment of active structures at the top of MCS-based similarity search results. With respect to overall and early enrichment performance, FMCS outperforms most of the seven other VS methods considered in these tests.

fmcsR is freely available for all common operating systems from the Bioconductor site http://www.bioconductor.org/packages/devel/bioc/html/fmcsR.html.



Comments

Dotmatics User Group Meeting

As you may have noticed I’ve written a variety of scripts for Vortex in the Tutorials section, if you would like to find out more about this and the other software packages available it might be worth you attending the free Dotmatics User Group Meeting.

http://www.dotmatics.com/ugm-registration/

The software has been coming on very impressively and this is the ideal opportunity to see what it is now capable of delivering.

Update As an aside I've been told that if you answer the question "How did you hear about the UGM?" with "Chris told me there was cake" there might be a nice surprise ;-)



Comments

Insights for data analysis

Insights is a self-organising data modelling tool that is particularly useful for noisy or fuzzy data.

som_3

Insights makes optimal use of the 64-bit processing power of your machine utilising all available cores in modern desktop machines.

speedup_2

The cost is $80-$2000 depending on the version, and there is an education discount and a free trial. There also currently appears to be a discount code.

There is a comprehensive list of data analysis tools for Mac OS X here.



Comments

Regress+ v2.7 released

Regress+ v2.7 has been released
Univariate Data Modeling: Equations and Distributions

  • Plain textfile input
  • Equations, with or without uncertainties (weights)
  • Distributions, continuous or discrete data
  • Discrete data grouped or ungrouped
  • Datasets up to 4,294,967,295 points (minimum 7)
  • Up to 10 parameters
  • User-selected optimization criterion (where appropriate)
  • Least squares
  • Minimum average abs(residual)
  • Maximum likelihood
  • Minimum K-S statistic
  • Minimum chi-square statistic
  • Full, dated Report (textfile)
  • Robust goodness-of-fit testing for distributions
  • Tunable precision
  • [Optional] State-of-the-art (BCa) central confidence intervals (90, 95 and 99 percent)
  • Tunable precision
  • High-quality (PDF, PNG) plots with one keystroke!
  • X/Y plot, with or without error bars
  • PDF plot
  • CDF plot
  • Probability plot for goodness-of-fit (see above)
  • [Optional] Logarithmic axes (when appropriate)
  • Editable axis labels
  • Automatic tick marks/labels (see above)
  • [Optional] Predictions for unobserved values or percentiles
  • With confidence intervals if desired
  • [Optional] Constant parameter(s)
  • 21 Built-in Equations
  • Plus user-defined model
  • [Optional] Test residuals for systematic error
  • [Optional] List data with fitted estimates and residuals
  • [Optional] Simulated-annealing mode for initial parameter estimates
  • 59 Built-in Distributions
  • 9 continuous, symmetric
  • 27 continuous, skewed
  • 11 continuous mixtures
  • 6 discrete
  • 6 discrete mixtures
  • [Optional] Creation of synthetic samples
  • No hidden assumptions anywhere
  • No approximations, apart from those common to sampling and bootstrapping generally
  • No data transformations of any kind
  • Extensive documentation
  • Data Modeling with Regress+ (PDF, 100 pages, 43 figures, 14 tables)
  • Compendium of Common Probability Distributions (PDF, 136 pages, 59 figures, also published separately)
  • Sample input and output files
  • Completely free! No cost, no license, no registration.

There is a list of data analysis tools here.



Comments

Wizard 1.3.6 released

Wizard 1.3.6 is a minor bug-fix and feature release now available in the Mac App Store.

Here's the list of changes:

  • Support for batch-importing multiple files of the same type
  • New: Count Distinct Values function in the Pivot view
  • Fix minor issues with importing from XLS files
  • Pro only: Support for importing .dta files created with Stata 13

There is a list of data analysis tools here



Comments

A comparison of 6 javascript chart plotting packages

Fusion Charts have provided a very useful comparison of 6 javascriptHTML5 chart plotting libraries.

The six libraries are FusionCharts Suite XT, HighCharts, Google Chart Tools, Sencha ExtJS, Charts, Chart.js, Flot, jqPlot. I’ve used Flot a couple of times and found it a very useful lightweight library. But as they say choice is good.



Comments

aiSee node graphing software

I’ve just added aiSee to the table of data analysis tools for MacOSX.

aiSee is node graphing software that automatically calculates a customizable layout of graphs specified in GDL (Graph De­scription Language). This layout is then displayed, and can be interactively explored, printed, and exported to various formats. There are free, academic and commercial licenses.



Comments

R and Python

If you are planning to use R with Python for handling a large amount of data then this blog post may be of particular interest, Stepping up to Big Data with R and Python: A Mind Map of All the Packages You Will Ever Need.



Comments

mathStatica updated

mathStatica 2.7 for Mathematica 9 has just been released.

This update contains Totes amazeballs automated Plotting, Piecewise Processing Engine, another 40 univariate distributions to the built-in palettes, mathStatica 2.7’s parallel processing engine unleashes the power of your computer — automatically — featuring phenomenal speed and power for users with multi-processor machines. There are also a number of new functions, and the pallets have been updated.

There is a page of data analysis packages here.



Comments

ChemmineR updated

ChemmineR a cheminformatics package for analyzing drug-like small molecule data in R was recently updated. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures.

To install, start R and enter

source("http://bioconductor.org/biocLite.R")
biocLite("ChemmineR")



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A couple of updates

The point and click data analysis tool Wizard Pro has been updated. In particular this update address a couple of issues

  • Preserve filter selections when switching between tables
  • Correctly parse numbers surrounded by spaces in CSV files 
  • Fix a bug where a blank header cell in an Excel spreadsheet caused subsequent columns not to be imported 
  • Fix some issues with PDF export of model images
  • Fix a crash when stacking tables with indicator variables

The Reference Management package Bookends has also been updated,

  • Get DOI was updated to deal with changes made by CrossRef
  • This includes dealing with changes made in the way CrossRef encodes accented characters.
  • Updated Import From Existing Bibliography to deal with changes made by CrossRef
  • Updated Bookends browser to detect DOIs on the Google Scholar web site to deal with changes made by Google



Comments

R reaches version 3.0.0

R the language and environment for statistical computing and graphics has now reached version 3.0.0.

Whilst there is a list of new features and updates, those listed as most significant are shown below.

  • Packages need to be (re-)installed under this version (3.0.0) of R.
  • There is a subtle change in behaviour for numeric index values 2^31 and larger. These never used to be legitimate and so were treated as NA, sometimes with a warning. They are now legal for long vectors so there is no longer a warning, and x[2^31] <- y will now extend the vector on a 64-bit platform and give an error on a 32-bit one.
  • It is now possible for 64-bit builds to allocate amounts of memory limited only by the OS. It may be wise to use OS facilities (e.g. ulimit in a bash shell, limit in csh), to set limits on overall memory consumption of an R process, particularly in a multi-user environment. A number of packages need a limit of at least 4GB of virtual memory to load. 64-bit Windows builds of R are by default limited in memory usage to the amount of RAM installed: this limit can be changed by command-line option --max-mem-size or setting environment variable RMAXMEM_SIZE.
  • Negative numbers for colours are consistently an error: previously they were sometimes taken as transparent, sometimes mapped into the current palette and sometimes an error.

There is a list of data analysis packages for MacOSX here.



Comments

Wizard Updated

Wizard the point-and-click statistical analysis for Mac has been updated.

The focus of this release is supporting several new import formats, including the oft-requested XLSX and Numbers document formats.

A major change in the product line is that reading and writing R files and generating R code has now "graduated" from the Pro version and is now available in the Standard version. But Pro users shouldn't feel left out: with this release, Support for importing binary SAS files and generating SAS code -- both features only available in the Pro version.

New Features:

  • Import XLSX spreadsheets
  • Import Numbers documents

New Features (Pro Version):

  • Import SAS binary files (.sas7bdat)
  • Import plain-text data with SAS commands (.sas)
  • Generate SAS model estimation commands

New Features (Standard Version):

  • Import/export R files
  • Generate R commands

Bug fixes

  • Fix a crash when zero observations are included in the Model view
  • Fix a bug when importing multiple sheets in XLS documents
  • Fix a bug where Q-Q plots were not properly exported as PDF

There is a listing of data analysis tools for the Mac here.



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A Review of StarDrop 5.3

I’ve just written a review of Stardrop an application from Optibrium that was designed to aid decision making for scientists involved in drug discovery that has recently been updated.

  • Virtual Library Enumeration – The Nova plug-in module for StarDrop now has the added ability to quickly and easily enumerate a virtual library based on a template scaffold that you define with substitution points and variable fragments. You can sketch the groups to substitute at each point, select them from a user-defined or centrally administered library, or take them from a decomposition of another series using the R-group analysis tool in StarDrop
  • Data visualisation - now allows you to apply interactive filters to your graphs and plots to quickly focus on the most interesting compounds. StarDrop now also supports the analysis of dates allowing you to explore variations of properties or scores with time
  • Clustering - this new tool enables you to easily identify groups of similar compounds within a data set, based on either their structural similarity or properties
  • Dataset Filtering - this helps you to remove compounds from a data set with unwanted sub-structures or property values. You can define any number of criteria with which to filter a data set
  • Duplicate Removal - when combining compound data from multiple sources it’s common to end up with multiple copies of the same compound in a single data set. The duplicate removal tool makes it easy to find these and choose the entries that you want to keep.
  • ADME QSAR – new model for predicting log([Brain]:[Blood]) (the old model remains available for consistency with previously calculated results)
  • StarDrop now includes a FieldAlign module, using Cresset's molecular Field technology, provides a unique, 3-dimensional (3D) insight into the biological activity, properties and interactions of your compounds.

There is a comprehensive list of software reviews here.



Comments

Chartsmith added to list of data analysis tools

I’ve just added Chartsmith to the list of data analysis tools.

Chartsmith is the premier charting and graphing application for Mac OS X. Built from the ground up on Mac OS X technologies, this application will make you and your data hum. Whether for scientific data visualization, for business presentation, or for graphics publishing, Chartsmith makes charting and graphing quick and easy.

scitech2

Chartsmith supports a variety of chart types and can import from Excel or ascii text files. There is also Applescript support for automating workflows.

There is a comprehensive listing of data analysis tools for Mac OS X here.



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ElementalDB

Way back in the distant past when I first joined the Pharma industry I remember working with a dumb terminal running sub-structure queries on a remote mainframe that seemed to take for ever on our relatively modest corporate database, returning the results would then bring our network to a crawl much to the annoyance of my colleagues. I’ve just downloaded ElementalDB from Dotmatics, this an iPad application that does a substructure search of a 1,200,000 structure database in less than a second.

Read more here.



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Wizard Pro updated

The data analysis tools Wizard and Wizard Pro have been updated to improve blank cell detection during excel imports.

Wizard supports the most common statistical tests and models, including...

Univariate Tests Shapiro-Wilk test of normality , 1-sample Kolmogorov-Smirnov (normality and uniformity) , Pearson's goodness-of-fit (equal proportions)

Bivariate Tests Pearson's goodness-of-fit (chi-square) , t-test and ANOVA , Correlation (Pearson product-moment) and R² , Mann-Whitney and Kruskal-Wallis , 2-sample and N-sample Kolmogorov-Smirnov

Multivariate Models Linear regression (OLS) , Weighted linear regression (WLS) , Poisson and geometric regression , Logistic regression (Logit) and Probit , Multinomial Logit and Ordered Probit , Negative Binomial (NegBin-2) , Cox Proportional Hazards

Regression Features Fixed effects , Robust standard errors , Clustered standard errors , Joint significance tests , Odds ratios , Residual analysis , Interactive prediction assistant

There are many more data analysis tools for Mac OS X here.



Comments

WaveMetrics Updates

XOP Toolkit 6.30 is now shipping. This release adds support for Xcode 4.3.2 through 4.6 and for Visual C++ 2012. This release is mostly to keep up with Xcode 4 changes and to add Visual C++ 2012 sample XOPs and documentation. As described in the release notes (Appendix C of the XOP Toolkit 6 manual), a side-effect of keeping up with Xcode 4 is that XOPs compiled by XOP Toolkit 6.30 require Igor Pro 6.20 or later. The requirement of Igor Pro 6.20 is the reason for bumping the XOP Toolkit version from 6.02 to 6.30. "6.30" was chosen because that is the contemporaneous Igor version. If you are a licensed XOP Toolkit 6 user, this is a free update.

IGOR Pro 6.3 has been updated.

New Features

Added a Batch Curve Fitting package: allows you to fit batches of data to the built-in or user-defined fitting function of your choice. A "batch" is a collection of similar data sets stored in waves to which a common fitting function, initial conditions, and weighting and masking waves have been applied. Each data set may be stored in a waveform, an XY pair, or in the columns of a 2D wave. Added the Scatter Dot Plot Panel. Scatter Dot Plots are one part category plot, one part scatter plot, and one part histogram. Like category plots they show total counts for multiple data sets, each labeled on the X axis. Like scatter plots they provide a sense of the data's distribution. Like histograms they sort data into bins of points in which all values fall into a range. The Multipeak Fitting 2 package now supports constraints on peak coefficients. NewImage supports direct RGBA color image plots. The FilterFIR notch filter length had been limited to 4001 points. Now the limit is 2147483647 points, which makes the minimum notch width 0.000107% of the sampling frequency.

There is a page of data analysis tools here.



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Scripting Vortex 12

In the previous tutorial we made use of the Virtual Computational Chemistry Laboratory web service to calculate aLogP and LogS, both these results were returned in a simple text format. More recently there has been an increased use of JSON format for data exchange.

JSON, or JavaScript Object Notation, is a text-based open standard designed for easy human-readable data interchange. It is derived from the JavaScript scripting language for representing simple data structures and associative arrays, called objects. Despite its relationship to JavaScript, it is language-independent, with parsers available for many languages including including C, C++, C#, Java, JavaScript, Perl, Python.

Molinspiration provide a number of cheminformatics tools but also provide a RESTful web service these web services can be used to calculate a range of molecular properties and bioactivity predictions.

The output from both web services is available either as a JSON string or plain text, the web service can be accessed by submitting a URL

Full details of the script are here.

vortex1



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Cheminformatics on a Mac

I gave a talk at the Cambridge Cheminformatics meeting last week, I’ve put the slides here. It was more of a demonstration than a talk but the slides give an overview and links to the various tools.

Slide01

Updated

A couple of people have asked for a pdf version of the slides for download.



Comments

Scripting Vortex:- Accessing a web service

I’ve just added the latest script for Vortex.

In previous scripts we have generated data using a local Java program, C program, PERL script, and SVL program. In this tutorial rather than have a local application generate the data we will use a web service.

mols

There are more scripts on the Hints and Tutorial pages.



Comments

StarDrop 5.3 is now available

Optibrium have just announced that StarDrop 5.3 is now available, including many new features, the highlights include:

  • Virtual Library Enumeration – The Nova plug-in module for StarDrop now has the added ability to quickly and easily enumerate a virtual library based on a template scaffold that you define with substitution points and variable fragments. You can sketch the groups to substitute at each point, select them from a user-defined or centrally administered library, or take them from a decomposition of another series using the R-group analysis tool in StarDrop
  • Data visualisation - now allows you to apply interactive filters to your graphs and plots to quickly focus on the most interesting compounds. StarDrop now also supports the analysis of dates allowing you to explore variations of properties or scores with time
  • Clustering - this new tool enables you to easily identify groups of similar compounds within a data set, based on either their structural similarity or properties
  • Dataset Filtering - this helps you to remove compounds from a data set with unwanted sub-structures or property values. You can define any number of criteria with which to filter a data set
  • Duplicate Removal - when combining compound data from multiple sources it’s common to end up with multiple copies of the same compound in a single data set. The duplicate removal tool makes it easy to find these and choose the entries that you want to keep.
  • ADME QSAR – new model for predicting log([Brain]:[Blood]) (the old model remains available for consistency with previously calculated results)



Comments

RapidMiner 5.3 released

RapidMiner v5.3 has been released. RapidMiner provides data integration, ETL, data analysis, and reporting in a single application, with an intuitive, drag and drop visual environment for designing and deploying customized analytical processes, and has been downloaded by over three million users worldwide.   In addition to over 100 performance, usability and stability improvements, the new version delivers more powerful data analysis operators and access to popular data sources including Microsoft Excel™ 2007 and SAS™. RapidMiner v5.3 is also fully integrated with the Rapid-I Marketplace, where users can discover and install new RapidMiner extensions published by a growing list of independent developers. Popular extensions include text and web mining, image mining and recommenders. Various Extensions for RapidMiner are available from the update server (go to the "Help" menu and select "Update RapidMiner")

RapidMiner v5.3 also features

  • More than 20 new functions for analysis and data handling, including multiple new aggregation functions;
  • File operators, including Move File, Rename File, Copy File, Create Directory, and Delete Files, directly from RapidMiner; and
  • A macro viewer that shows macros and their values in real time during process execution, for better debugging.

There is a comprehensive list of data analysis tools for Mac OS X here.



Comments

DataGraph 3.1 released

I just noticed that DataGraph has been upgraded to version 3.1

DataGraph is a simple and powerful graphing application for Mac OS X. It is a great companion for Excel, Numbers or any of the big statistical packages. Simple because it is very easy to draw plots, bar graphs, and fit functions. Start typing in data and the graph immediately shows up. Pick from the initial template list and modify the data, change colors, resize easily and interactively.

Included on the page of data analysis tools



Comments

Data Extractor Updated

Data Extractor solves the problem that often advanced users have, the necessity to extract data available in text format on one or more files (often thousands and thousands of files) , and moving them inside a table or a database in an ordered and structured form with fields and records for archiving and successive processing. Data extractor can parse thousands and thousands of file in few seconds and collect all the data inside these files using simple instructions on how to recognise data, how to extract them and where to put these data inside Data Extractor tables, ready to be exported

Included on the page of data analysis tools


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Maple 16.02 released

Maple 16.02, a maintenance update, is available to all users running Maple 16. This update contains enhancements to many areas, including:

  • Maple 16 now works on Macintosh OS X 10.8
  • Connectivity features have been extended to include: MATLAB® 2012b and Microsoft Visual Studio 2012

  • Physics. Enhancements were made to several areas of the Physics package, including

  • Algebraic manipulations of dot products of quantum operators (possibly tensorial) and eigenstates
  • Algebraic simplification taking into account commutation/anticommutation rules
  • Simplification of tensor products involving the sum rule for repeated indices in the presence of symmetric and antisymmetric tensors
  • Dagger, Commutator, AntiCommutator, Bracket
  • Normal forms of products of quantum operators
  • Saving and loading Physics setup across sessions
  • Allowing selective partial clearing of setting using Setup(clear, <…>)
  • Copying and pasting of textbook display (typesetting = extended)

  • Enhancements were made to memory management/garbage collection.

  • Improvements were made to the display of data tables and to custom palettes.

I’ve updated the page of data analysis tools


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Tableau Mobile

A few days ago I mention Spotfire for the iPad and a couple of readers sent in details of similar applications.

Tableau mobile is an iPad front-end to an analytics server. Create interactive reports and dashboards in Tableau Desktop then publish them to Tableau Server for secure access on your desktop, or on the web or with your iPad.

Similarly SAP BusinessObjects Mobile connects to the SAP BusinessObjects Business Intelligence platform.

Comments

Spotfire for iPad

Spotfire for the iPad requires access to a TIBCO Spotfire Web Player Server. By default, the app is connected to our public demo gallery so you can start experiencing data in Spotfire immediately. After that, you can connect to your internal server, or you can connect to public servers and explore Spotfire analytical tools.

spotfire

Now added to the mobile science page.

Comments

Mathematica 9 is released

Wolfram have announced the release of Mathematica 9 with a host of new features

  • Optimize your workflow with the Wolfram Predictive Interface The Wolfram Predictive Interface makes it easy to find and use the power of Mathematica 9. The Input Assistant's context-sensitive autocompletion and dynamic highlighting help you discover and enter commands, and the next-computation Suggestions Bar offers optimized suggestions for what to do next. It's the next step in our ongoing Compute-as-You-Think initiative that began with free-form linguistic input.

  • Examine social networks with built-in links to social media Mathematica 9 introduces a full suite of social network analysis features including community detection, cohesive groups, and centrality measures, plus built-in links to Facebook, LinkedIn, Twitter, and more. It also adds new capabilities for network flows and new graph distributions.

  • Work with systemwide support for units Mathematica 9 introduces a new unit system containing more than 4,500 different units, all integrated with Wolfram|Alpha's sophisticated unit interpretation system. From unit conversion to dimensional analysis, Mathematica provides you with all the tools you need to work with, and extract properties from, units and quantities.

  • Use survival analysis, random processes, and other expanded capabilities in data science and visualization Mathematica offers more statistical distributions than any other system, including specialized coverage of finance, medicine, and engineering. Mathematica 9 adds survival and reliability analysis; full support for random processes including queues, time series, and stochastic differential equations; a complete set of customizable gauges for dashboards and reports; and systemwide support for automatic legends for plots and charts.

  • Integrate R code into your Mathematica workflow Mathematica 9 offers built-in ways to integrate R code into your Mathematica workflow, allowing data exchange between Mathematica and R and execution of R code from within Mathematica. With RLink, R users can use thousands of functions from across the full Mathematica system.

  • Deploy interactive documents with enhanced capabilities Instantly create documents in the Computable Document Format (CDF) to present interactive charts of results, show dynamic models, or prototype your next application, and deploy them to the web or desktop. With Mathematica Enterprise Edition, you can deploy CDFs with live data and other enhanced features.

  • Perform powerful 3D volumetric and out-of-core image processing Mathematica 9 scales up performance to very large 2D- and 3D-volumetric images using out-of-core technology, and builds in a hardware-accelerated rendering engine for 3D images and volumes. Mathematica 9 also adds feature tracking, face detection, image enhancements, and other highly optimized algorithms to perform comprehensive image analysis.

  • Use integrated analog and digital signal processing Filter and analyze sound, images, and multidimensional data with Mathematica 9's signal processing capabilities. Instantly design and deploy interactive filters and simulate them with Wolfram SystemModeler.

  • Visualize with new customizable gauges and built-in legends Mathematica 9 adds a complete set of customizable interactive gauges for dashboards and reports, with built-in support for units. Systemwide support for automatic legends for plots and charts means legends with any style or layout can be added to arbitrary content.

I’ve updated the page of data analysis tools

Comments

Wizard Pro 1.1.1

Wizard Pro has been updated this release fixes a critical bug that prevented saved multivariate models from opening on Mountain Lion. Wizard Pro is $199.99 for Mac OS X 10.6 through 10.8 and is only available in the Mac App Store. Wizard Pro is a multivariate statistics program for data analysis and exploration. The software keeps all work (tables, results, predictions) in a single document with an iTunes-like navigator and provides "interactive interfaces" for querying data. It includes basic statistics tests, regression models and results, stacking and joining of tables, indicator variables with custom logic, and more.

There is a page of data analysis tools here.

Comments

Addded TOPCAT to data analysis tools

I’ve added TOPCAT to the list of data analysis tools.

TOPCAT is an interactive graphical viewer and editor for tabular data. Its aim is to provide most of the facilities that astronomers need for analysis and manipulation of source catalogues and other tables, though it can be used for non-astronomical data as well. It understands a number of different astronomically important formats (including FITS and VOTable) and more formats can be added. It offers a variety of ways to view and analyse tables, including a browser for the cell data themselves, viewers for information about table and column metadata, and facilities for 1-, 2-, 3- and higher-dimensional visualisation, calculating statistics and joining tables using flexible matching algorithms

I also noticed that Venuz has been updated

Veusz is a GUI scientific plotting and graphing package written in Python. It is designed to produce publication-ready Postscript or PDF output. SVG, EMF and bitmap export formats are also supported. The program runs under Unix/Linux, Windows or Mac OS X, and binaries are provided. Data can be read from text, CSV or FITS files, and data can be manipulated or examined from within the application

Comments

PublishPlot has been updated

PublishPlot has been updated and is now available from the Mac App store, it is a very handy tool for creating publication quality plots from any text based table of data.

PublishPlot is scriptable using either Applescript or Python.

New in version 1.1 is a tool bar to display x,y location when hovering over a plot, new fitting options and the ability to apply mathematical transforms to any two curves. There are also new export functions and bug fixes.

PublishPlot is included on the page of data analysis tools

Comments

MagicPlot Viewer

Sometimes you just need to have a quick look at a data file and Magic Plot Viewer offers the means to do this.

  • Supports text files with different structure
  • Auto detection of column delimiter and decimal separator
  • Multiple columns for X and Y can be set
  • All MagicPlot data navigation tools (zoom, hand, scrolling...)
  • Equal scale for all thumbnails can be set
  • Shows data point coordinates in status bar
  • Quick export and printing of plots
  • Additional support of image files (PNG, GIF, JPEG, BMP)
  • Fullscreen mode

Added to the data analysis tools page

Comments

Viewing Docking results in Vortex using Astex Viewer

I recently wrote a review of ForgeV10 from Cresset in which I actually imported the results into Vortex to do the analysis. There were however two issues with doing this, firstly interpretation of the 3D structures is sometimes difficult, this can be resolved by creating a 2D rendering of the structure. The other issue is trying to interpret the docking pose whilst looking at the analysis of the results in say a Vortex scatter plot.

I’ve been working with Mike Hartshorn and the people at Dotmatics who have incorporated OpenAstexViewer (a 3D molecule viewer) into the application you can read the full article here..

Comments

Wizard Pro

I’ve just added Wizard Pro to the page of data analysis tools.

Wizard Pro can Import spreadsheets and CSV, plus files from SPSS: .sav, .por, and .sps files, Stata: .dta and .dct files, R: .RData files. EExport data as CSV and JSON, plus files for SPSS: .sav binary files, Stata: .dta binary filesR: .RData binary files. It can generate regression commands suitable for verifying results in SPSS, Stata, and R, It is fully multi-core — regressions run instantly and supports millions of rows and thousands of columns — no hard limits.

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Vortex script exchange

Vortex is an advanced data analysis package that understands chemistry, the capabilities of Vortex can be extended by the use of scripts. I’ve now created Vortex script exchange that users can use to download or share scripts.

There are also a series of scripting tutorials here to provide a starting point for creating new scripts.

Hopefully these scripts will be valuable to you.

Comments

Scripting Vortex 9

I recently wrote a review of ForgeV10 in which I imported the results into Vortex for analysis. This works fine the only issue being the resulting structures are 3D which makes interpretation of the structure sometimes difficult to discern, this script uses OpenBabel to create SMILES which can be rendered as 2D images.

Comments

iOS and OS X Graphing Library

iOS and OS X Graphing Library Free For Development

VVI today announced the availability of it’s graphing library for iPhone, iPad, iPod touch and Macs. Version 10.8.3 of the graphing libraries and frameworks, aka Vvidget Code, brings the following achievements:

  • Supports deployment to OS X versions 10.6 to 10.8 (Macs) and iOS versions 4.3 to 5.1 (iPhone, iPad and iPod Touch).
  • Supports development on OS X versions 10.6 to 10.8 and Xcode 3.2 to 4.4.1.
  • Uses native API on deployment platforms for the fastest and most robust possible implementation. That is, Cocoa Touch for the iPhone, iPad and iPod Touch and Cocoa for the Mac.
  • Use for development is free.
  • Eleven Vvidget-based applications available from VVI on the iTunes App Store for iPhone, iPad and iPod Touch and on the Mac App Store demonstrate Vvidget Code in actual situations.
  • Applications based upon Vvidget Code are free-standing and require no additional installs. Vvidget Code itself can be installed using package installers or shared using free-standing Xcode projects.
  • Download and install instructions are at: Download And Install Vvidget Code

Please email sales@vvi.com for additional information.

Comments

PublishPlot

I’ve just added PublishPlot to the page of data analysis tools.

PublishPlot Features

  • Quickly convert any table of data into a plot
  • Customize all features of the plot
  • Easily scale the plot to any size while conserving relative sizes of plot features
  • Annotate the plot with labels and arrows
  • Add error bars
  • Do simple data transformations including fits and spline interpolations
  • Plot arbitrary functions of x
  • Edit data in PublishPlot by simple plain-text editing methods
  • Export a plot to a PDF file (or simply drag it to your desktop or to another application)
  • Create and transform plots using AppleScripts or Python scripts

PPExample1

Comments

Mjograph Updated

MjoGraph is an X-Y graph editor that runs on Mac OSX or on other platforms with Java. It is well customized for researchers, especially in the field of science, whose research work includes computer simulations and visualization of their numerical results.

There are many more data analysis tools listed here

Comments

StarDrop update released

A new version of StarDrop is now available. The new features include

  • FieldAlign – this new module, using Cresset's molecular Field technology, provides a unique, 3-dimensional (3D) insight into the biological activity, properties and interactions of your compounds, helping to guide the design of novel, potent compounds with a high chance of success, there is a review of the FieldView and FieldAlign here.
  • R-Group analysis – analyse a chemical series to interactively visualise the impact of variations to R-groups, linkers, atoms or fragments on compound properties. Explore the SAR of your chemistry, identify new optimisation strategies and automatically enumerate the missing combinations
  • ADME QSAR – new models for predicting 2C9 pKi, BBB category and P-gp category (the old models remain available for consistency with previously calculated results)
  • Nova – now available with the ability to select compounds using a combination of properties and chemical diversity

screen-glowing

Comments

StarDrop 5.2 coming soon

Optibrium have just announced the imminent release of the next version of StarDrop

The highlight of this new release is the addition of a new plug-in module that provides access to Cresset's FieldAlign™ technology, which offers a unique, 3-dimensional insight into the biological activity of your compounds. This new development is the first result of the technology exchange, between Optibrium and Cresset, and adds another powerful tool to StarDrop that will enable you to understand the three-dimensional (3D) structure activity relationship (SAR) of your chemistry Version 5.2 also introduces new enhancements of StarDrop's core capabilities, in particular a flexible tool for performing automatic R-group analysis. This new feature analyses a chemical series to interactively visualise the impact of variations to R-groups, linkers, atoms or fragments on compound properties to help chemists to further understand the SAR of their chemistry and identify new optimisation strategies

There are reviews of StarDrop and FieldAlign on the software reviews page and a listing of data analysis packages here.

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A Review of CheS-Mapper

I’ve just completed a review of CheS-Mapper.

CheS-Mapper (Chemical Space Mapper) is a 3D-viewer for chemical datasets of small molecules, a recent publication in the Journal of Chemiformatics describes the application DOI: 10.1186/1758-2946-4-7, In addition more information is available on the wiki page. Whilst there are many applications for the visual analysis of data, very few provide the tools needed to handle chemical structures, CheS-Mapper is a java application that runs under Mac OSX (I only tested Lion) based on the Java libraries Jmol, CDK, WEKA, and utilizes OpenBabel and R, that provides an interesting means to explore chemical data sets.

CheSMapper2

There a complete list of software reviews here.

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Using Flot and Chemical Identifier Resolver

I recently wrote a couple of Applescripts that use the Chemical Identifier Resolver (CIR) a web service that performs various chemical name to structure conversions and it occurred to me that is should be possible to use this service to generate images for use as popups on a graph in the same way that I’ve previously described using Flot and ChemSpider. This works well but relies on the structure already being in the ChemSpider database, for novel structures we need a service for generating the image from a chemical identifier. CIR provides a simple web service for doing exactly this, for example submit a SMILES string and it can return a 2D image.

This tutorial shows how to create an interactive plot using Flot and CIR

Comments

Data Extractor

Data Extractor allows to extract data from files and collect them ready to be exported for later use Data is collected in records with custom specified fields inside an internal table. Data can be exported at any time. Data extractor can parse thousands and thousands of file in few seconds and collect all the data inside these files using simple instructions on how to recognise data, how to extract them and where to put these data inside Data Extractor tables, ready to be exported and transferred to a database.

There is a comprehensive list of data analysis applications for the Mac here.

Comments

Stardrop Review

I’ve just posted a review of Stardrop an application from Optibrium that is designed to aid decision making for scientists involved in drug discovery.

Comments

Vortex script for MayaChemTools

I’ve just added a new Vortex script, this one uses a PERL script that is part of the excellent MayaChemTools.

Scripting Vortex Using OpenBabel
Scripting Vortex 2 Using filter-it
Scripting Votrex 3 Using cxcalc
Scripting Vortex 4 Using MOE
Scripting Vortex 5 Calculating similarities using OpenBabel
Scripting Vortex 6 Filtering compounds
Scripting Vortex 7 Using MayaChemTools

Comments

Added JTreeView to data analysis tools

JTreeView renders gene expression data into several interactive views.

Comments

Dotmatics LinkedIn Group

Thos who use LinkedIn might be interested to see that Dotmatics now have a dedicated group.

http://www.linkedin.com/groups/Dotmatics-4327915?

I wrote a review of the Dotmatics tools a while back and have written a series of scripts for Vortex.

Comments

MagicPlot

I’ve just added MagicPlot to the list of data analysis tools.

MagicPlot looks like a useful plotting/fitting tool that is free for students.

  • Publication-quality customizable X-Y plots with multiple axes
  • Handy nonlinear fitting
  • Visual multi-peak fitting
  • Powerful text table import dialog with plot preview
  • Data manipulation
  • FFT, integration, differentiation, histograms, descriptive statistics (Pro)
  • Auto recalculation on data change (Pro)
  • Batch Processing without programming (Pro)
  • Plot scale navigation with mouse
  • Plot style templates (Pro)
  • Multi-level undo/redo with history

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Scripting Vortex 6

I’ve just added another Vortex script. In this script we will make use of the ability of filter-it to categorise input molecules into 1) a set of molecules that fulfil all criteria as defined in the filter definition file (passed molecules), and 2) a set of molecules that do not fulfil at least one of the defined filter criteria (failed molecules). The filter file defines the criteria for acceptable calculated phisicochemical properties and also any substructures that should be included or excluded during the filtering. The filter file is a simple text file that users can define for themselves, there is a detailed explanation on the silicos-it website. They also provide several example filters “Leadlike”, “Druglike”, “CMCLike” and “Clean” which cleans up a file without imposing a “drug like” filter. It should be relatively straight-forward for users to create their own filters, one could imagine a rule-of-3 filter that might be used in fragment-based screening approaches, or a toxicphore filter based on SMARTS shown to be implicated in a specific toxicity. It might also be possible to define project specific filters if a project requires a specific profile. If you need help it might be worth contacting Silicos-it.

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VVI Graph SDK

VVI® today announced the availability of Vvidget Code, its Graph SDK for iPhone, iPad and Mac, version 10.7.6, bringing the following improvements:

The features are extensive and shown by the Graph app on the iTunes and Mac App Store. All the graphs in those applications are now available in the new version. See the links: Graph for iPhone, iPad and iPod touch and Graph for Mac to install those applications and test the Vvidget Code Graph SDK.

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iOS:Chart

A chart & graph library for iOS and Mac OS X developers.

  • Fully native Objective-C library for direct, easy use in any iOS XCode project.
  • Several samples and demo projects to make integration and getting started a snap.
  • Over 50 powerful graph types, including bar, line, area, pie, scatter, bubble and waterfall.
  • An easy-to-use yet powerful object oriented API gives you full control over your charts with a minimum of effort.
  • Real 3D graphs with controls to zoom, pan, rotate and skew!
  • Adjust and control every element on every chart. Multiple Y-axis, depth effects, reference lines, scale controls and much more.
  • The full power of the PGSDK (charting library of choice for MicroStrategy, IBM/Cognos and many more) now for your mobile application!

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Scripting Vortex 5

I’ve just posted the latest tutorial on scripting the chemically intelligent spreadsheet application Vortex, this tutorial shows how to use OpenBabel to provide similarity searching.

The full list of Vortex scripting tutorials are shown below.

Scripting Vortex Using OpenBabel
Scripting Vortex 2 Using Sieve
Scripting Votrex 3 Using cxcalc
Scripting Vortex 4 Using MOE
Scripting Vortex 5 Calculating similarities using OpenBabel

More hints and tutorials can be found here.

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Scripting Vortex

This is the fourth tutorial on scripting Vortex a chemically intelligent data visualisation package. In the previous tutorials we have looked at getting data from OpenBabel, sieve, and cxcalc in this tutorial we will be using MOE as the compute engine. MOE from Chemical Computing Group is probably best known as a graphical user interface to a suite of computational chemistry tools, whilst this is indubitably the means by which many users will interact with the program it is worth finding out about the command-line tools that are available. These tools are often accessed by pipeline tools such as Knime to allow rapid processing of large files. CCG provides four very useful command-line tools in particular sddesc allows the calculation of some or all of the MOE molecular descriptors for each molecular entry.

The Vortex Scripts

Scripting Vortex Using OpenBabel
Scripting Vortex 2 Using Sieve
Scripting Votrex 3 Using cxcalc
Scripting Vortex 4 Using MOE

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DataWrangler

You might also want to look at Data Wrangler for an online tool for cleaning up data.

There is a comprehensive list of data analysis packages that run under Mac OSX here

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Graph version 10.7.3 available

VVI® today announced the availability of Graph version 10.7.3 on the Mac App Store, bringing the following improvements:

  • Copy paste is now implemented for textual (labels) table cells and columns.
  • Column paste now accepts many number delimiters such as blank, comma, tab, Return, etc.
  • Added Save and Open Panels to export and import data into tables.
  • Added a main title to the pie chart.
  • Arrow keys now move the table cell editor to the expected adjacent cell instead of move the text cursor.
  • When a sheet is present, ESC and Command-. shortcuts dismiss (cancels) the sheet.
  • When the cell editor is used to enter an empty value in the last row of a column then that column length is reduced by one except when the data needs to be rectangular (as in the Z-Values table).
  • ESC dismiss (cancels) the cell editor without entering the data.
  • Made many small adjustments to the user interface to make it look and perform better.
  • Implemented elemental table behaviour in the backend.

There is a list of data analysis applications here

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A Review of Data Creator

I’m occasionally asked for is a test data set that can be used to evaluate an application. Whilst I keep a couple of data sets that I can use perhaps Data Creator will provide a more comprehensive solution.

Data Creator is an application that has been designed to fill this important niche, Data Creator can be used to build very large data sets using field types defined by the user and then filled with random realistic content. I’ve just added a review of Data Creator.

There is an increasing collection of software reviews here.




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KNIME User Group Meeting

I just got this message:-

“Following our very successful user meeting and workshops in 2011, we will be holding a similar event in 2012. The 5th KNIME Workshop and Users Meeting will take place between January 30 and February 3, 2012 at Technopark in Zurich, Switzerland. Early bird registration closes on Jan 15th. You can register here .

There is a KNIME tutorial here.


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Data Creator

I’ve compiled a list of data analysis tools and sometimes when I’m just trying a new application out I need a set of random data. Data Creator looks like it might be ideal for those sort of occasions, it can create structured data table (fields) and fill them with random proper content (records) with a single click. These data can be saved on disk and imported into databases and applications for test and demonstration purposes. Data Creator can be used to create very large data sets (thousands and thousands of records) for stress test of structures and scripts.


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Added Solo to list of Data Analysis tools

Solo software equips users to perform PLS, PCA and many other multivariate analyses in a stand-alone, point-and-click environment.

Key Features:

  • Data Exploration and Pattern Recognition (Principal Components Analysis (PCA), Parallel Factor Analysis (PARAFAC), Multiway PCA...)
  • Classification (SIMCA, k-nearest neighbors, PLS Discriminant Analysis, Support Vector Machine Classification, Clustering (HCA)...)
  • Linear and Non-Linear Regression (PLS, Principal Components Regression (PCR), Multiple Linear Regression (MLR), Classical Least Squares (CLS), Support Vector Machine Regression, N-way PLS, Locally Weighted Regression...)
  • Self-modeling Curve Resolution, Pure Variable Methods (Multivariate Curve Resolution (MCR), Purity (compare to SIMPLSMA), CODA_DW, CompareLCMS...)
  • Curve fitting and Distribution fitting and analysis tools Instrument Standardization (Piece-wise Direct, Windowed Picewise, OSC, Generalized Least Squares Preprocessing...)
  • Advanced Graphical Data Set Editing and Visualization Tools
  • Advanced Customizable Order-Specific Preprocessing (Centering, Scaling, Smoothing, Derivatizing, Transformations, Baselining...) Missing Data Support (SVD and NIPALS)
  • Variable Selection (Genetic algorithms, IPLS, Selectivity, VIP...)

There is a listing of data analysis tools for Mac OS X here.

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Using Calculation Fields in Vortex

Whilst Vortex has tools that allow you to do some analysis and of course you can use the scripting facility to access statistical or model building packages like R in this tutorial we will be using a model taken from the literature and implementing it within Vortex using a calculation field to construct the algorithm.

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KnowledgeMiner (yX) for Excel 2.9.1 update

Self-organizing, Parallel, High-Dimensional Modeling now for Excel 2011! New Features of KnowledgeMiner (yX) for Excel version 2.9.1 [New] Improved Charting. Now displays actual vs. predicted data on both predicted and learning data. [update] Tutorial updated.

There is a list of data analysis and plotting tools for Mac OS X here.


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Aabel Updated

Aabel v3.0.6 complimentary update is optimized for the newest Mac OS X version, Lion. In addition to optimizing Aabel v3 for Lion, this update also includes fixes for all known bugs and glitches that have been discovered up-to-date. The performance of Aabel v3 has been enhanced on Lion; this is in particular noticeable on machines with modern graphic cards. The updater that is downloaded from this page can be used on both Snow Leopard and Lion, but the performance-related enhanced aspects of the application are Lion-specific.

There is a comprehensive list of data analysis packages that run under Mac OSX here

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Scripting Vortex 3

ChemAxon's Calculator (cxcalc) is a really useful command line program in Marvin Beans and JChem that performs chemical calculations using calculator plugins. There are a lot of calculations provided by ChemAxon (e.g. charge, pKa, logP, logD), and others can be added by writing custom plugins, perhaps one of the most useful is the ability to calculate the acidic and basic pKa. Calculation of pKa is essential to get a reasonable hold on the LogD of a molecule. LogD is probably the most critical physicochemical property in drug discovery, it has a major influence on absorption, cell penetration, metabolism, CYP450 inhibition and induction, PGP transporter activity and activity at the HERG channel, and is often a critical component of any structure activity relationship.

These scripts make use of cxcalc to generate data columns in Vortex

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DAQ Plot has been revised to v10.7.2

I just got this email

This is a one-time email to let you know that DAQ Plot has been revised to v10.7.2 with these new features:

  • Runs on Mac OS X 10.6 (Snow Leopard) and 10.7 (Lion).
  • Implements up to 16 y-axis time and spectral graphs.
  • Implements the default microphone as an enumerated hardware unit.
  • Implements direct printing.
  • Implements color legend on the main window.
  • Implements pop over window for data discovery.
  • Includes many adjustments to the user interfaces, general bug fixes and speed improvements.

As it turns out, many customers are delaying upgrading to Lion so this newer version supports both Lion and Snow Leopard as well as makes many significant improvements. Because of this change (the Snow Leopard version was previously EOL, but now is not) we are taking the step of this email to inform you of this current version.

For instructions on upgrading your version of DAQ Plot please email support@vvi.com.

There is a list of data analysis and plotting tools for Mac OS X here.

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InfiniteGraph Added to data analysis list

I just added InfiniteGraph to the list of data analysis applications.

InfiniteGraph is a distributed graph database written in Java (with a C++ core), is interoperable across Linux, Windows and Mac OS/X platforms, and can also be deployed in most virtualized cloud environments. InfiniteGraph is available in both free and licensed versions. The free version does everything the licensed version does, up to 1 million nodes and edges, and can be expanded almost infinitely.

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mathStatica 2.5 for Mathematica 8

mathStatica 2.5 for Mathematica 8 includes a new parallel processing engine affording huge performance gains.

mathStaticaParallelTimings

Timings in seconds using Mathematica 8.0.4 (latest Oct 2011 release) running on a Mac Pro computer.

For more data analysis tools look at the Data Analysis Applications page.

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Vvidget Builder is now available

Vvidget Builder is now available in the Mac App Store:

http://itunes.apple.com/us/app/vvidget-builder/id470597599?mt=12

You may also be interested in the movies:

Shows how to use Vvidget Builder:

http://www.vvidget.org

Shows how to program a Vvidget Code application for the iPhone using Xcode 4.2:

http://www.vvidget.org/develop
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StarDrop 5.1 will be available for Mac

StarDrop 5.1 will be available for Mac Read More...
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Free Vortex Webinar

Free Vortex Webinar Read More...
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Vvidget Builder beta for Lion

Vvidget Builder beta for Lion is now available for use Read More...
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Data analysis tools

Data Desk has been updated. Read More...
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Aabel Updated

The high performance data analysis and plotting application Aabel v3.0.6 has been updated Read More...
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EnSight Updated

EnSight Updated Read More...
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VVI Graphing beta

VVI today announced the start of a beta period for it’s graphing applications and libraries Read More...
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KnowledgeMiner (yX) for Excel version 2.8

KnowledgeMiner (yX) for Excel version 2.8 has been released offering performance improvements. Read More...
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More data analysis tools for Mac OS X

I’ve just added a four new applications to the Data Analysis Tools web page

RapidMiner, SciDAVis, LabPlot, fityk
Read More...
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Data Analysis tools

I’ve updated the data analysis tools page. Read More...
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DataGraph Updated

DataGraph has been updated to version 2.3.1 Read More...
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Knime and XQuartz updated

Knime and XQuartz updated

Read More...
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Getting Data

Graph digitizer software Read More...
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More Data Analysis tools

More updates to the Data analysis tools Read More...
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Data Analysis tools

I’ve just added friedEgg Touch to the list of 60 data analysis tools available for Mac OS X. Read More...
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Mathematica 8.0

Mathematica has been updated to version 8 with a host of new features. Read More...
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Knowledge Miner (yx) updated

Knowledge Miner (yx) has been updated to take advantage of multi-processor machines. Read More...
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DataAnalysis

Added DataAnalysis a general purpose iPad App for the plotting and analysis Read More...
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R Updated

R version 2.12.0 has been released Read More...
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Added XLSTAT

Added XLSTAT to the page of Data Analysis Tools. Read More...
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Aabel Update

Gigawiz have announced an update to Aabel Read More...
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DeltaGraph Update

DeltaGraph 6 is about to be released.

Read More...
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Knime

I’ve added Knime to the list of data analysis applications. Read More...
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KnowledgeMiner (yX) for Excel updated

KnowledgeMiner (yX) for Excel is a knowledge mining tool that works with data stored in Microsoft Excel to build predictive and descriptive models. Read More...
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Aabel Updated

The powerful data analysis and plotting tool Aabel 3 has been updated (version 3.0.4).

Read More...
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Data Analysis Tools

Updated the page of Data Analysis tools Read More...
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KNIME Desktop for Mac OS X

  • Highly experimental version of KNIME 2.1 released for Mac OS X.
Read More...
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Top MacInChem Searches

Top search terms used on MacInChem. Read More...
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KnowledgeMiner (yX) for Excel

KnowledgeMiner (yX) for Excel is a knowledge mining tool that works with data stored in Microsoft Excel Read More...
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Aabel Updated

Aabel updated for Snow Leopard Read More...
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Vvidget Updated

Vvidget a chart and graphing system for OS X has been updated. Read More...
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Maple Updated

Maple 13 has been updated.

Read More...
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Stata 11 released

Stata 11 has been released. Read More...
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R updated

The statistical programming and plotting library R has been updated. Read More...
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DataGraph 2.0 Update

DataPlot has been updated to version 2.0. Read More...
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Developers needed

Developers need for project related to the use of the novel technologies in Snow Leopard (including OpenCL and Grand Central) on Nehalem-based Mac Pros to build a Cocoa/Objective C-based large-scale data analysis and visualization application for scientific numerical and image data. Read More...
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MATLAB R2009a beta for 64-bit Intel-based Macs is now available

MathWorks MATLAB R2009a beta for 64-bit Intel-based Macs is now available Read More...
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Update for Aabel

Update for Aabel Read More...
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StatPlus:mac Updated

AnalystSoft has updated StatPlus:mac adding several new features and graphics. Read More...
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Updates

Mathematica home edition and CLC Main Workbench Read More...
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EnSight

I’ve added EnSight to the list of Data Analysis tools
Read More...
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News Updates

A collection of software updates Read More...
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Aabel Review

  • A new review of the statistics, data analysis and plotting application Aabel.
Read More...
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Vortex Review

An update to Vortex. Read More...
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R Updated

R has been updated to version 2.8 Read More...
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Maple Updated

The heavy-weight mathematical modeling tool Maple has been updated. Read More...
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Vortex: Cheminformatics data analysis

I’ve just added a review of Vortex a cheminformatics tool import files in a variety of formats, it provides depiction and structure based searching, together with property calculations tightly integrated with excellent charting and analysis tools. Read More...
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Solver now available

Solver for Microsoft Excel is available again. Read More...
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StatPlus:mac updated

StatPlus:mac has been updated. Read More...
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Updated Stats site

The MacStats site has been updated and is moving to a dedicated URL, http://www.MacStats.org. Read More...
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Molegro Data Modeller

Molegro Data Modeller is a cheminformatics application for Data Mining, Data Modelling, and Data Visualization.

Read More...
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Statsplus:mac

Turn Excel into a proper statistical analysis tool. Read More...
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Aabel

Gigawiz announces a new release of Aabel. Read More...
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SPSS 16 available

A new version of SPSS is available.

SPSS is one of the real heavyweights in the statistical analysis area but the Mac version lagged behind. It now looks like version 16 brings a major upgrade for Mac users
Read More...
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Data Analysis Tools

I've just added Regress+ to the page of data analysis tools. Read More...
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Aabel updated

Just in from Gigawiz, Aabel updated for Leopard. Read More...
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proFit updated

ProFit updated for Leopard. Read More...
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Aabel

Aabel has been updated Read More...
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