Macs in Chemistry

Insanely Great Science

Scripting the Organic Chemistry Reference Resolver

The Organic Chemistry Reference Resolver is an invaluable web service that takes as input a text reference to a published article in a variety of formats and then finds and displays the corresponding publication.

The real beauty of a web service is that it can be accessed via a variety of means, including an applescript. This applescript uses as input either text that has been copied to the clipboard or the text the user has typed into a text box, it submits the request to the web service and displays the result in the web browser.

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MOE 2011 Review

I’ve just added a review of the latest version of MOE from Chemical Computing Group.

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An alternative to the Delete Restore folder applescript

Matt over at MacOSX Tips has sent me an alternative script, in this rather than deleting the restore file it is simply enabled or disabled. This script demonstrates the implementation for Safari.

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Delete Restore folders for selected applications

One of the new features in Lion is the ability of applications to resume activity at the point an application was quit. This means that when you reopen an application it will open and display all the documents you were editing in the state when you quit the application. This is obviously very useful but there are times when you may not want confidential documents automatically opened and displayed when you open an application.

This Applescript allows you to delete the restore folder for specified applications.

There are more applescripts here.

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Don't automatically restore documents when opening applications

One of the new features in Lion is the ability of applications to resume activity at the point an application was quit. This means that when you reopen an application it will open and display all the documents you were editing in the state when you quit the application. This is obviously very useful but there are times when you may not want confidential documents automatically opened and displayed when you open an application.

As far as I can tell there is no option to switch this off in an application by application basis so the best option might be to switch this off feature off completely. In the “General” section of the “System Preferences” uncheck the box labelled “Restore windows when quitting and re-opening apps”.

restore

Hopefully developers will update applications to do this on an application by application basis.

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Atomic Dashboard added

I’ve just added the Atomic Dashboard which features an interactive periodic table that lets you explore the chemical elements -- their properties, periodic trends, history, and relevance to society. And more exciting, with its new 3D Molecule Library and its physics-based, 3D models of atomic orbitals, molecules, compounds, gases, and crystals, you can explore the relationships between the behavior of atoms and molecules and their 3D structure.

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Atoms in Motion

I’ve added Atoms in Motion a fully interactive atomistic simulation that uses sophisticated Molecular Dynamics (MD) algorithms to perform computational chemistry calculations right on your iPad to the Mobile Science page.

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MOE 2011.10 released, Lion compatible

CCG have announced the release of MOE 2011.10. This includes a new license manager compatible with LIon.

Some of the new and enhanced features in MOE include:

================================================================

Non-Bonded Interaction Visualization Model - Visualize halogen bonds, H-bonds, CH-X, proton- for interactive modeling - Calculate strengths using Extended Hckel Model - Display strengths and interactions in 2D Ligand Interaction Diagrams Sequence Editor Redesign - Wrapped view, zoom, chain name/tag, etc. - Synchronized coloring (% identity, similarity, Clustal X, RMSD) - Cut and paste for loop grafting, inserting linkers, filling gaps, etc. Combinatorial Build in Pocket - Add R-groups to one or more attachment points in 3D pocket - Apply 2D and 3D filters, refine in (flexible) pocket and score - Use Builder to scan fragments for interactive ligand optimization Analysis of Solvent in Binding - Calculate within minutes a solvent binding free energy map using 3D-RISM - Calculate water, salt and hydrophobe solvation densities in complex or apo receptor - Diagnose how well alternate groups take advantage of water upon binding Macromolecular System Preparation - Correct common problems in protein structures automatically - Browse alternate conformations, cap termini, build missing loops - Optimize hydrogen bond network by flipping residues and adjusting states GPCR Family Database and Alignment Tools - Identify and annotate transmembrane regions of GPCRs - Add alignment constraints to improve GPCR sequence alignments - Augment a database of GPCR crystal structures with in-house data


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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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Protein Ribbons display tutorial

I’ve corrected the broken links in the Protein Ribbon Models of Proteins tutorial using the ChemDoodle Web Components.

There are more tutorials here and a selection of software reviews here.

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Recent MMDS improvements: drawing and renderinge

The Mobile Molecular DataSheet (MMDS) v1.3.7 has had a bit of attention to the sketching interface, and now makes available the most commonly used small ring templates from the context menu:

There is a page of mobile apps for science here

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Eyescale announces the release of GPU-SD 1.0.

GPU-SD is a library and daemon for the discovery and announcement of graphics processing units using ZeroConf. It enables auto-configuration of ad-hoc GPU clusters and multi-GPU machines. GPU-SD is used by the upcoming Equalizer 1.2 release for automatic configuration of local and remote GPU resources.

Version 1.0 of GPUSD provides automatic local discovery for Linux (X11/GLX), Mac OS X (CGL, GLX) and Windows (WGL, WGLNVgpuaffinity, WGLAMDgpu_association), a simple network announcement daemon using DNS service discovery and ZeroConf networking as well as remote discovery of resources announced using the GPU-SD daemon.

GPU-SD is a cross-platform library, available for Linux, Windows and Mac OS X and supports both 32-bit and 64-bit execution. It is licensed under the LGPL open source license, which allows free usage in commercial and open source projects. For more information about GPU-SD, please visit http://www.equalizergraphics.com/gpu-sd

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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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New major release of Molegro Virtual Docker

Molegro is pleased to announce a new major release of Molegro Virtual Docker, an integrated platform for computational drug design available for Windows, Linux, and Mac OS X. Molegro Virtual Docker offers high-quality protein-ligand docking based on novel optimization techniques combined with a user interface experience focusing on usability and productivity.

Major new features in version 5.0: -GPU-accelerated docking on CUDA supported hardware making it possible to screen drug-like compounds up to 30 times faster than using conventional CPU-based methods. The GPU implementation builds upon and extends the research described in the paper "GPU-Accelerated High-Accuracy Molecular Docking using Guided Differential Evolution" (http://dl.acm.org/citation.cfm?id=2001576.2001818). -The new 2D Ligand Map provides an easy way to inspect and visualize protein-ligand interactions.

For more information, or to download a trial version, please visit our company website at: http://www.molegro.com


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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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JSDraw updated

JSDraw™ is a chemical structure editor/viewer built in 100% Javascript, running on all platforms, including Windows, Mac, Linux, iPad/iPhone, Android tablets/phones and Chromebooks. JSDraw 1.3.0 release includes following improvements and changes:

  1. The js file is renamed to Scilligence.JSDraw.js
  2. Speeded up JSDraw on IE 6/7/8 by adopting Silverlight
  3. Added fragment-selecting tool ( http://www.scilligence.com/web/fragment-selecting-tool-in-jsdraw-1210.aspx )
  4. Improved drawing performance
  5. Being able to expand Amino Acid using right click menu ( http://www.scilligence.com/web/bio-features-expanding-amino-acid.aspx )
  6. Bug: atom labels overlaps bonds
  7. Added Bracket object to support polymers ( http://www.scilligence.com/web/polymer-features-comes-to-jsdraw-1210.aspx )
  8. Added Lasso selecting tool ( http://www.scilligence.com/web/jsdraw-lasso-selecting-tool.aspx )
  9. Widely supporting SGroup ( http://www.scilligence.com/web/sgroup-in-jsdraw.aspx )
  10. Being able to Set object colors


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KNIME Updated

KNIME (Konstanz Information Miner) is a user-friendly and comprehensive open-source data integration, processing, analysis, and exploration platform. From day one, KNIME has been developed using rigorous software engineering practices and is used by professionals in both industry and academia in over 60 countries.

Release Date: December 1, 2012 Enhancements

  • Enh 2933: Database Schema Browser for Database (Connection) Reader nodes
  • Enh 2924: Database (Connection) Reader allows executing multi-line SELECT and non-SELECT queries
  • Enh 2976: New Database dialog "Connection" tab more user friendly UI
  • Enh 2952: Node-Annotations (multiline labels) replacing one-line labels underneath a node
  • Enh 2882: Sort data in table view by clicking the column header
  • Enh 2914: TableView supports Ctrl-C on a single cell
  • Enh 2959: Tips & Tricks dialog is shown when KNIME starts
  • Enh 2934: New editor action that allows to align nodes vertically (in addition to align horizontally)
  • Enh 2928: Automatic checks for updates during startup (added command line argument "-checkForUpdates")
  • Enh 2840: Missing Value node multiple column selection in Individual tab
  • Enh 2876: Resolved Rename node name confusion: new name: Column Rename
  • Enh 2975: Decision Tree View has zoom functionality
  • Enh 2980: Weblog Reader is now able to read compressed files
  • Enh 2974: File browsers in reader nodes (SDF, CSV, etc.) open with directory of currently selected file
  • Enh 2907: XPath node can return missing value instead of empty string/NaN for non-matches
  • Enh 2908: XPath node allows returning of attributes in a node set (multi-matches)
  • Enh 2937: SubsetMatcher node allows mismatches
  • Enh 2878: Add hidden debug option to initialize sorter memory service
  • Enh 2883: Added ability to parallelize computation in ColumnRearranger
  • Enh 2958: Added #clearHistory method for FileChooserHistory
  • Enh 2964: Color chooser DialogComponent and SettingsModel is added
  • Enh 2271: Upgrade of CDK integration (better renderer, SMARTS parsing) - part of community extensions

There is a KNIME Tutorial here

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CoLocalizer Pro added to alphabetical listing

CoLocalizer Pro is a quantitative colocalization analysis software. It calculates specialized coefficients to characterize colocalization of fluorescence markers objectively. The software works with images produced by all major manufacturers of fluorescence confocal microscopes.

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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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ReadCube added

I’ve just added ReadCube to the reference management page.

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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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CLiDE Updated

CLiDE is a chemistry intelligent equivalent of Optical Character Recognition (OCR) software. Just as an OCR can recognize characters from a scanned images of printed text, CLiDE can recognize structures, reactions and text from scanned images of printed chemistry literature. The software saves users hours of redrawing structures from printed material, as it transforms the 'images' into a 'real structures' that can then be input into databases.

The new and improved features of the latest release include:

  • support for Windows, MAC and Linux operating systems
  • improved structure recognition capability
  • improved error reporting
  • improved processing of document pages which contain tables, underlined text and page separator lines that touch a few letters
  • extended input format support with Word (DOC and DOCX) and HTML
  • extended export format support with CML and MRV formats
  • integrated support for ChemAxon's Marvin Sketch, Accelrys'Draw and ChemDraw editors
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Molegro Virtual Grid

Molegro Virtual Grid creates an infrastructure for distributing docking runs on multiple machines. By simply installing the MVG agent on a computer, its resources can be used transparently by the grid controller. Virtual Grid support is built into Molegro Virtual Docker: for instance, to dock a library of compounds against a receptor, simply setup a compound data source, and select 'start job on Virtual Grid' in the Docking Wizard. Molegro Virtual Grid is multi-core aware and can be installed on any platform: Linux, Windows, and Mac. The machines in the grid do not need to run the same operating system. Now added to the alphabetical listing

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Website Update

As I’m sure you will have noticed the site is undergoing a major upgrade, I hope to complete the update by the weekend until then please bear with me ;-)

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RSC Mobile

RSC Mobile is a mobile app which provides up-to-the-minute access to RSC journals. Full text HTML and PDF access via wireless networks for subscribing institutions/organisations. The latest news from the RSC Publishing Platform. Ability to save articles for offline reading - and to save the abstract for articles where the reader doesn't have full text access. Sharing of content via email, Twitter or Facebook.

There is a page of mobile apps for science here

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Scripting Vortex 2

This is the second page on scripting Vortex, on the first page I described how to use OpenBabel to calculate a limited selection of chemical properties. In this script we will use one of the brilliant tools from silicos.

SIEVE is a program for filtering out molecules with unwanted properties. It is based on the Open Babel open source C++ API for rapid calculation of 45 different molecular properties.

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WebGL on mobile devices

Are you fed up by the number of times you visit a web page and find you don’t have the plugin/applet to view the content? Or lost count of the times you have to update because of plugin security updates or applet java versions. Well you might like this post from iChemLabs. They have a demo of WebGL running on a mobile device.

We recently started optimizing our 3D ChemDoodle Web Components for mobile browsers, and will be fully supporting WebGL on all mobile platforms that implement it. This will allow scientists to quickly and affordably use the web to reach large numbers of users to reduce the cost of education and further spread science, especially when using the open-source and free ChemDoodle Web Components library. We already have the 3D components running on iOS and Android devices”

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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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Website feedback

Many thanks for the feedback I’ve had over the last couple of days.

I’ve added an interactive Periodic Table (application/applet), updated details on several applications and corrected many typos and spelling errors.

Also thanks to funding from the NSF SI2-SSE program (NSF1047875 & NSF1047919) and close collaboration with NVIDIA a major performance update to Amber was released August 18th 2011 for the GPU accelerated PMEMD package.

The new version of SMARTCyp includes a specific CYP2D6 model and improved reactivity for benzothiophene sulfurs. A paper describing the CYP2D6 model has also been published in ACS Medicinal Chemistry Letters. http://pubs.acs.org/doi/abs/10.1021/ml200246f

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Update to AppleScriptObjC Explorer

Version 1.1.0 is now available. It includes several localizations, more frameworks, and the ability to check for and install updates. See http://www.macosxautomation.com/applescript/apps/runner.html for details.

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XQuartz 2.7.0 released

The XQuartz project is an open-source effort to develop a version of the  X.org X Window System that runs on Mac OS X. Together with supporting libraries and applications, it forms the X11.app that Apple has shipped with OS X since version 10.5.

X11 2.7.0
Released: 2011.11.04
This release contains xorg-server 1.11.2
Installation
Download XQuartz-2.7.0.dmg (Snow Leopard and Lion), and open it with Mac OSX's Installer.
Important Notices
OS-X Requirements
OS-X 10.6.3 or later is required to install this package.

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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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Release of FieldStere V3.0

Cresset have announced the release of a new version of popular bioisostere replacement tool, FieldStere.  FieldStere is a fast and powerful software tool which uses Cresset’s innovative field-point technology, together with a database of molecular fragments, to help guide drug discovery projects and generate new intellectual property.  Version 3.0 includes impressive updates to the science and user interface, and constitutes the most significant scientific update to FieldStere since its introduction.

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Macs In Chem RSS Feed

I’ve been asked about the RSS feed for the MacInChemBlog.

I’ve changed the feed link for Feedburner so if you subscribed using that all should be OK. Other readers may need to click on the link on the left as highlighted in the image below.


I’ve also changed the comments from Echo to DISQUS.
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VVI® today announced the start of a beta period for its data acquisition application, DAQ Plot.

VVI® today announced the start of a beta period for its data acquisition application, DAQ Plot. During this period, users may participate in the following ways:

- Buy DAQ Plot direct from VVI or the Mac App Store and provide feedback to
support@vvi.com for the beta and upcoming version.

- Sign a Non-Disclosure Agreement and then receive beta versions in an iterative fashion to speed the introduction of your desired features and also discuss non-released software and features with the expert in data acquisition on Mac OS X.

The beta is intended to facilitate the introduction of features that radically improve DAQ Plot products. Here are just a few issues and ideas:

- DAQ Plot currently only supports two y axes. The new version supports sixteen y axes. This is important to data acquisition plotting because acquired signals can have very different units and hence scales. To plot each signal on a different scale requires a good multi-coordinate graph representation.

- In addition to the present data acquisition devices, the new DAQ Plot supports plotting from the default microphone included on each Mac computer.

- Many user interface adjustments have been made to make DAQ Plot the best data acquisition strip chart application on Mac OS X. As you can imagine a 16 coordinate graph might be overwhelmingly complex, but because everything is automatically done it is as easy as flipping a switch (or in this case one pop up button per signal).

- The manual (
http://www.vvidget.org/manuals/DAQPlot) is good but can be better. The user manual is currently undergoing a rewrite during this beta.

Due to the confidential nature of the beta, most improvements are non-public. There are many issues yet to be factored and this is a good opportunity for users to provide feedback. For additional information email
sales@vvi.com

For additional information consult the following links:

http://www.vvidget.org/daq
http://www.vvidget.org/manuals/DAQPlot
http://www.vvidget.org
http://www.vvidget.org/news
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SAR Table added to mobile science page

SAR Table designed for creating tables containing a series of related structures, their activity/property data, and associated text. Structures are represented by scaffolds and substituents, which are combined together to automatically generate a construct molecule.

There is a page of mobile apps for science here
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Macinchem website Update

As you probably know Apple are dropping support for MobileMe based websites and so I’ve had to move “Macs in Chemistry” to a new web host. I’ve taken the opportunity to clean up many of the links and pages but as you can imagine after nearly 10 years of posts using multiple packages to generate the pages it was getting a little untidy.
So feel free to kick the wheels, take it for a drive and explore the site.

If you find any problems please let me know, and if you have suggestions or contributions I’d be delighted to hear from you.
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Mobile apps for chemistry in the world of drug discovery

An extensive review of mobile apps that might be useful for scientists.

Mobile apps for chemistry in the world of drug discovery

Antony J. Williams, Sean Ekins, Alex M. Clark, J. James Jack, Richard L. Apodaca
Drug Discovery Today
Volume 16, Issues 21-22, November 2011, Pages 928-939

Mobile hardware and software technology continues to evolve very rapidly and presents drug discovery scientists with new platforms for accessing data and performing data analysis. Smartphones and tablet computers can now be used to perform many of the operations previously addressed by laptops or desktop computers. Although the smaller screen sizes and requirements for touch-screen manipulation can present user-interface design challenges, especially with chemistry-related applications, these limitations are driving innovative solutions. In this early review of the topic, we collectively present our diverse experiences as software developer, chemistry database expert and naïve user, in terms of what mobile platforms could provide to the drug discovery chemist in the way of applications in the future as this disruptive technology takes off.


There is a page of
mobile apps for science here
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Gains for Mac and iOS share.

The latest net market share is available from Net Applications.

There is a big surge in Mac usage up half a percent to 6.95% this increase is at the expense of Windows now down to 91.86%.
Over the last 12 months Mac usage has risen from 5.1% to 6.95% an all time high. Mac usage in North America is now 13.32%.

In the mobile/tablet arena iOS continues to dominate, now up to 61.6%, JavaME the long time main rival has now fallen to 12.8% and is now behind Android at 18.9%. As might be expected after all the recent problems Blackberry usage drops to 2.48%.
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Scripting Vortex

Read More...
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Mac Users in business are more productive

Three years ago, research firm Forrester said "Windows is the only desktop you need support."

Not any more.

As Fortune first reported
yesterday, Johnson called Mac users the "heavy hitters" and "heroes" in organizations, Forrester suggests that the typical Mac user fits in the segment it calls "power laptop" users, who work an average of 45 hours a week and make 44% more money. "Most of the Macs today are being freewheeled into the office by executives, top sales reps, and other workaholics."

Read more:
http://www.businessinsider.com/mac-users-are-more-productive-2011-10#ixzz1cHHuepkH
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OSIRIS Property Explorer

I recently came across a website that may be of interest,

The OSIRIS Property Explorer shown in this page is an integral part of Actelion's inhouse substance registration system. It lets you draw chemical structures and calculates on-the-fly various drug-relevant properties whenever a structure is valid. Prediction results are valued and color coded. Properties with high risks of undesired effects like mutagenicity or a poor intestinal absorption are shown in red. Whereas a green color indicates drug-conform behaviour.
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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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PubGet for iPad

PubGet for iPad delivers full text journal articles straight to your iPad Read More...
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Gaussian pages updated

Gaussian pages updated Read More...
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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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Siri knows Chemistry

Siri knows Chemistry Read More...
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OpenBabel updated to 2.3.1

OpenBabel updated to 2.3.1 Read More...
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Visual model building on your iPad

Visual model building on your iPad Read More...
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Steve Jobs and Apple revolutionized the way scientists render their work

Nature editorial on Steve Jobs Read More...
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Scripting ChemBioDraw

A script to convert .cdx to .png file format Read More...
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iNMR progress on new version

I just got this message from the developer of iNMR Read More...
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Major increase in Mac share

Mac market share Read More...
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Free Vortex Webinar

Free Vortex Webinar Read More...
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Amber on GPU

Amber usage survey Read More...
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NMR shift Database

nmrshiftdb2 is a NMR database 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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OpenCL in scientific computing

I was at the Cresset UGM yesterday and saw an excellent talk by Simon McIntosh-Smith describing their work porting the docking software Bude (that was originally written in a mixture of Fortran and C++) over to OpenCL.

The performance gains were very impressive, what was equally striking was the efficiency gains as measured by electricity usage, it looks like several thousand pounds will be saved for every million compound docking run.

He also showed the portability of OpenCL code, allowing efficient use of both the GPU and CPU.

He has a report on “The GPU Computing Revolution” available online

https://ktn.innovateuk.org/web/mathsktn/articles/-/blogs/the-gpu-computing-revolution


If you would like to learn more Apple have a
OpenCL section in the Developer library, and Simon’s website is an invaluable resource, and there a couple of recommended books (links to Amazon)







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Chemical Fingerprints

chemfp is a free set of command-line tools, and the underlying Python software library, for generating cheminformatics fingerprint files and searching them based on Tanimoto similarity. Read More...
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AppleScriptObjC Explorer 2.1 released

A free update to AppleScriptObjC Explorer Read More...
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FieldTemplater released on the Mac

FieldTemplater released on the Mac Read More...
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Mobile apps for chemistry in the world of drug discovery

Mobile apps for chemistry in the world of drug discovery Read More...
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WebMO version 12 released

WebMO version 12.0 has been officially released Read More...
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HPC Mac OS X

HPC on a Mac Read More...
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Mac share continues to rise.

Latest data from Net Applications Read More...
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Data analysis tools

Data Desk has been updated. Read More...
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Mobile Science

Added a presentation to the Mobile Science Page. Read More...
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Design a drug competition

DaM-Header

Cresset is running the third competition to find the world’s most creative chemists. The challenge is simple – find the most bioisosteric molecule to a reference compound that we provide. To help you on your way we will provide a free demo license for FieldAlign and FieldView that is valid for the duration of the competition, a reference molecule and a starting molecule to be adapted. Interested? Simply enter here to receive everything you need.
The catch – we want you to design structurally diverse molecules that are still reasonably chemically tractable and drug-like.
Our next challenge will be another anti-malarial target, a farnesyl transferase inhibitor which is a 1000 fold selective for plasmodium falciparum and the available X-ray structure of this compound bound to the Human form from PDB: 3E32.  We would like you to design a new core for the published ligand using FieldAlign. To help you, we will give you access to FieldAlign together with all the files that you need and we’ve produced an introductory video and a detailed explanation of the steps that you need to take. Interested in winning the iPad2?
Register now.
Once you have designed your entry, just enter into the form
here or send it to support@cresset-group.com.
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ChemSpider Mobile

ChemSpider Mobile allows you to search the ChemSpider chemical database Read More...
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ChemDoodle Update

ChemDoodle 4 has been released and is now available. Included are hundreds of fixes and new features, recommended by customers. Read More...
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Teraflop-desktop Apple system

Teraflop-desktop Apple system Read More...
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Clipboard tools

Request for clipboard tools Read More...
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AppleScriptObjC Explorer 2

AppleScript Explorer 2 has been "officially" released Read More...
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AppleScriptObjC Explored

The third edition of 'AppleScriptObjC Explored' is out 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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KNIME has been updated

KNIME Desktop 2.4.1 can be downloaded from the download page Read More...
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ChemAxon US UGM

ChemAxon have announced the program and are calling for participants for ChemAxon's 4th US User Group Meeting (US-UGM) which will take place in San Diego, CA on September 27-28. Read More...
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XQuartz updated

XQuartz has been updated to version 2.6.3 Read More...
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The continued rise of iOS

Net Applications released the July market share analytics yesterday and we see yet more evidence for the migration to mobile platforms which now command 5% of the operating system market share. iOS that powers iPads and iPhones is now up to 3% up from around 1% twelve months ago.
Mac OS also increased to 5.61% up 0.24% on last months figure.
These gains are largely at the expense of Windows now down to 87.6%.
The same trend is seen for Web Browsers with IE down nearly 1% with Chrome up to 13.49% (+ 0.38%) and Safari 8.1% (+ 0.62%) showing major gains.
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Mobile Science Updates

SXSW Music downloads Read More...
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Added Crystal

CRYSTAL program computes the electronic structure of periodic systems

Read More...
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ChemDoodle and Lion

From the ChemDoodle website

“We have finished our testing of ChemDoodle on Mac OS X Lion, and everything works as expected. ChemDoodle will continue to work for you on your mac, even after you update to Mac OS X Lion.
We regard Mac OS X as a primary platform and will always support it. With ChemDoodle, you can be confident that your work will be unimpeded by major OS updates.”
osxlion-1
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J-ICE a Jmol Interface for Crystallographic and Electronic Properties.

J-ICE is a Jmol Interface for Crystallographic and Electronic Properties. Read More...
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Chemical Drawing

More javascript based chemical drawing packages Read More...
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Turbomole Updated

TURBOMOLE:  New Release 6.3 Read More...
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XCode and Absoft Pro Fortran Updated

XCode and Absoft Pro Fortran Updated Read More...
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A comparison of 6 chemical drawing packages

A comparison of the 6 chemical drawing packages available on ChemSpider Read More...
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EnSight Updated

EnSight Updated Read More...
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MassXpert updated

MassXpert has been updated.
Read More...
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Creating Lion boot disc

Creating Lion boot disc Read More...
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Lion compatibility

There is now a compatibility table wiki for Mac OS X Lion, I would encourage everyone to read and contribute. 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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Market Share

Net Applications released the June market share analytics yesterday. The gradual erosion of the Windows operating system continues with a 0.4% loss, the chief beneficiaries were Mac OSX up 0.05%, and iOS up 0.25% to now stand at 2.63%.
Looking at the Windows share XP continues to occupy >50% of the share.

It is a similar story on the browser front with IE declining with Chrome and Safari increasing.
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FieldAlign updated

Cresset announced the release of FieldAlign 3.0.1. Read More...
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MobileMe and iCloud

MobileMe to iCloud transition. 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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Mobile Science Page Updated

Mobile Science Page Updated Read More...
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Data Roaming

Since people will soon be embarking on their summer travels I thought I’d remind people to turn off data roaming whilst abroad Read More...
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Plotting in Instant JChem

Plotting in Instant JChem Read More...
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Chemistry Dictionary for Mac OS X

Chemistry Dictionary for Mac OS X Read More...
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OpenEye announce EON and ROCS updates

OpenEye has announced a couple of updates. Read More...
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ChEMBL Safari extension

ChEMBL Safari extension Read More...
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Net Applications market share

The latest monthly data is in from Net applications Read More...
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ChemAxon UGM

ChemAxon's US UGM, Sept 27-28, San Diego, CA  Read More...
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What do you want to see at WWDC2011?

What do you want to see at WWDC2011? Read More...
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sdf2xyz2sdf

sdf2xyz2sdf is an open-source software aimed at converting SDF files into TINKER XYZ files (and vice versa) 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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Getting data from a dead Mac

Getting data from a dead Mac Read More...
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Updated Mobile Science Page

Updated the mobile science page. Read More...
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QuantumBio Inc. and Chemical Computing Group, Inc. Announce the Release of the DivCon Discovery Suite for the Molecular Operating Environment (MOE)

 QuantumBio Inc., a leader in Structure-based and Fragment-based Drug Discovery solutions, based upon their next-generation linear-scaling quantum mechanics (QM) methods, has announced the release of DivCon Discovery Suite 5.0 for the Molecular Operating Environment (MOE) platform Read More...
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Smart Phones, a Powerful Tool in the Chemistry Classroom

Publication on the use of smart phones in the classroom. Read More...
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Interactive plots showing chemical structures

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 Read More...
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Mnova 7.0 released

MestreLab have announced the release of Mnova 7 Read More...
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Equalizer 1.0 and Collage 0.3.

Release of Equalizer 1.0 and Collage 0.3. Read More...
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ChemDoodle Mobile

ChemDoodle Mobile a calculator for drawn organic structures. Read More...
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Rosetta and Mac OS X 10.7 (Lion)

If you have been following any of the discussions about the next Mac OS X operating system (Lion) you may have noticed that Rosetta is no longer supported. Read More...
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iMolview

iMolview is an app for the iPhone and iPad that lets you browse protein, DNA, and drug molecules in 3D Read More...
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XQuartz 2.6.2 released

XQuartz 2.6.2 released Read More...
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DAQ Plot Version 10.6.11 Now Available

VVI® today announced DAQ Plot version 10.6.11 Read More...
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SYBYL-X now on Mac (updated)

SYBYL-X now on Mac Read More...
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Ball and Stick for iPad

Ball & Stick is a high-quality molecular visualization app for the iPad Read More...
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Big gains for Apple across the board

The latest data from Net Applications shows Apple had significant increases in market share across all the platforms. Read More...
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Yield101 added to mobile science page

Yield101 added to mobile science page Read More...
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Designing Cheminformatics apps for the iPhone

Basic primitives for molecular diagram sketching Read More...
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Apple Financial Update

Apple posted quarterly financial results today, showing earnings per share of $6.40, with record second quarter revenue of $24.67 billion and record second quarter net profit of $5.99 billion. Read More...
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MObile Reagents Updated

MObile REagents (MORE) updated Read More...
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Top Queries on Macs in Chem

Macs in Chemistry top search queries Read More...
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Updated T-Z section

Application Updates

I’ve now added over 30 new applications to the alphabetical listing and updated the details on 5 applications.

Read More...
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Updated Q-S section

Application Updates Read More...
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Yet more updates

Application Updates Read More...
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More Application Updates

Application Updates Read More...
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More Application Updates

Application Updates Read More...
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Application Updates

Application Updates Read More...
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OLN Chemistry LabNotebook

Chemistry LabNotebook Read More...
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ChemSpotLight

ChemSpotLight Update Read More...
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SQLVue special offer

SQLVue special offer Read More...
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Latest Market Share from Net Applications

  • Latest Market Share from Net Applications
Read More...
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Jamberoo molecule editor

  • Jamberoo (former JMolEditor) a java program for displaying, analyzing, editing, converting, and animating molecular systems.
Read More...
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UK Government should use Apple products.

UK Government should use Apple products. Read More...
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Apple WWDC 2011

WWDC sold out Read More...
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Fconv

  • Fconv is a command-line tool for several tasks concerning manipulating, converting, and analyzing data from different file formats
Read More...
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Chil² platform availabe on Macs

The Chil² platform offers a complete molecular modeling environment. Read More...
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iNMR Updated

iNMR Updated Read More...
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Cresset Announces Academic Access Program

Cresset Announces Academic Access Program Read More...
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Data Analysis tools

I’ve updated the data analysis tools page. Read More...
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XQuartz update

XQuartz updated Read More...
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silicos tools for Drug Discovery

silicos tools for Drug Discovery Read More...
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iBabel

Here is the latest version of iBabel (3beta3), Read More...
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ApplescriptObjC and XCode 4

AppleScriptObjC and XCode Read More...
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AppleScriptObjC Explorer

A new version of AppleScriptObjC Explorer available Read More...
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Reaction101

Reaction App for iPhone/iPad etc. Read More...
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Mobile Science

I’ve updated the mobile science page with a couple of new applications. Read More...
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AppleScriptObjC Explorer

AppleScriptObjC Explorer is a script editor that takes advantage of AppleScript's ability to call Cocoa methods in OS X 10.6 and later. Read More...
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Global Internet Usage Share

February Global Internet Usage Share Read More...
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ChemDoodle, WebGL and Protein Ribbons

A tutorial demonstrating the use of ChemDoodle and WebGL to display ribbons on proteins. Read More...
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FieldAlign Review

You can read the FieldAlign Review here.
Read More...
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Reference Management Applicatios

Papers2 is coming. Read More...
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A couple of Updates

ChemDoodle Web Components version 4.1 has been released and ctioga2 has been released a full rewrite of ctioaga, ctioga2 is a powerful command-line based polymorphic plotting program, based on the Tioga plotting library. Read More...
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Gabedit updated

The latest release 2.3.5 of Gabedit is now available Read More...
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Spectral Game

Tired of Angry Birds? Then why not try Spectral Game.

Read More...
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Building Safari Extension

A tutorial showing how to write Safari Extensions Read More...
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AppleScriptObjC Explored Updated

AppleScriptObjC Explored has been Updated Read More...
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Review of FieldView

A review of FieldView. Read More...
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iOS market share shows impressive gains

January global internet market share from Net Applications Read More...
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Applications Added

Alphabetical listings updated with new applications added. Read More...
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kSpectra Toolkit

kSpectra Toolkit for Mac OS X a set of powerful tools for advanced time series analysis.
Read More...
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DataGraph Updated

DataGraph has been updated to version 2.3.1 Read More...
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Pentalobe screws

There has been a minor storm in the tabloids in the UK about Apple using Pentalobe screws

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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iNMR version 4

iNMR is now at version 4 Read More...
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ChemDoodle Web Components 4

This latest update to the ChemDoodle Web Components brings a host of new features 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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Scripting the Script Editor

How to automate the Script Editor using Applescript Read More...
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CUDA Serious Security Flaw?

Potential CUDA security flaw. Read More...
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Mac OSX Update

Mac OS X update and the Mac App store Read More...
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ICM Update

Molsoft have announced an update to ICM. Read More...
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Structure searching using MMDS

Structure searching using MMDS Read More...
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Applescript and curl

Using Applescript and curl Read More...
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End of year internet market share

The end of year global internet market share data from Net Applications is now available. Read More...
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