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.

There a complete list of software reviews here.

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

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.

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.

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

JTreeView renders gene expression data into several interactive views.

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.

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

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.

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.

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!

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.

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

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

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

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.

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.

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.

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.

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.

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.

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

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

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.

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

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.

DeltaGraph 6 is about to be released.

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

• Highly experimental version of KNIME 2.1 released for Mac OS X.

Maple 13 has been updated.

• A new review of the statistics, data analysis and plotting application Aabel.

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