A while back I posted a script that copied a file to a users MobilMe Public folder and created an email link to that file. With the imminent demise of MobileMe a couple of people have asked me for a script that does the same but uses Dropbox.

This script shows how to copy a file to your Dropbox Public folder and then email a link to it.

SMARTCyp has been updated to version 2.1.1. SMARTCyp is a method for prediction of which sites in a molecule that are most liable to metabolism by Cytochrome P450 a major contributor to oxidative metabolism.

The latest update now includes models for prediction of CYP2D6 and CYP2C9 specific metabolism

A reader commented that they often emailed ChemBioDraw .cdx structures to colleagues who it turned out did not have a copy of ChemBioDraw to view them, whilst it is possible to convert the cdx file to other formats using OpenBabel they usually just ended up exchanging an image. They asked if there was a better solution and this is an ideal task for Applescript. This script assumes the structure you want to email is open in ChemBioDraw, it will create an email using Apple Mail containing the structure as a SMILES string, and embed the .cdx file together with an image in PNG format.

KosmicTask is an integrated scripting environment for Mac OS X. Whilst Mac OS X supports a number of scripting technologies either via it’s UNIX roots (Shell scripting , Perl etc.) or via Cocoa Framework Scripting using Apple’s scripting bridge (Applescript, Ruby, Python etc.) you can end up using a different script editor for each scripting language. KosmicTask allows you to script in a wide variety of languages from within a single editor. KosmicTask uses a plugin architecture that allows it to support a range of scripting languages, details of the languages supported by KosmicTask are shown below:-

• AppleScript
• AppleScript Cocoa - AppleScriptObjC
• Bash Shell
• C Shell
• C and C++
• F-Script Cocoa
• Java
• JavaScript
• JavaScript Cocoa - JSCocoa
• Korn Shell
• Lua
• Lua Cocoa
• PHP
• Perl
• Python
• Python Cocoa - PyObjC
• Ruby
• Ruby Cocoa
• Tcl
• Tenex C Shell
• Z Shell

KosmicTask also supports another very capable means of achieving automation - appscript. Appscript is supported by both Ruby and Python an alternative to the ScriptingBridge. 

It also allows sharing of scripts with other KosmicTask users via the local shared network.

I’ve also added it to the list of Applescript Resources.

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

This development release are now signed with an Apple DeveloperID for increased security.

Download XQuartz-2.7.2_rc2.dmg, and open it with OS X's Installer.

Full details of the changes are here.

Version 3.0 of the javascript chemical drawing package Xemistry Web Sketcher has been released.

This joins a list of javascript powered chemical drawing tools. It seems pretty fully featured but I have to confess I prefer a rather more minimalist interface with templates, elements available from menus. However drawing packages are very much a personal preference.

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.

IQmol is a free open-source molecular editor and visualization package. It offers a range of features including a molecular editor, surface generation (orbitals and densities) and animations (vibrational modes and reaction pathways).

One of the challenges of creating apps for mobile devices is making functionality available via the user interface and the limited real estate. The UI of the mobile molecular data sheet (MMDS) has been updated to addresses a minor but persistent inconvenience: previously, the main command bank had to be open in order to exit from any of the editor panels.

There is a listing of mobile science apps here.

I’ve added Chemistry Reference Resolver to the page of Safari Extensions. This adds a toolbar to your browser as well as adds a right-click menu option for reference resolving

When Apple released Safari version 5 one of the most important new features was the support for extensions. Extensions are a great way to add features to Safari to personalise web browsing, they enable the addition of features that you find useful. There is a listing of Extensions that might be useful for chemists and judging by the weblogs these are of significant interest. If you are working with them however it is a bit of a pain to check which are installed and which are enabled. This applescript is a very neat way of getting a report, it also serves as a demonstration of how to link to shell scripts, in particular using the unix command cat, a standard Unix utility that concatenates and lists files, to generate the report.

It has now been a couple of years since the human genome was first sequenced and we are now seeing companies offering personal genome sequencing. Illumina are now offering MyGenome an iPad app that allows you to explore a real human genome. In due course they hope to allow you to explore your own genome.

There is more information about the app here.

Now added to the mobile science page.

OpenEye has to announced the release of OEDocking v3.0.0. OEDocking is a suite of well-validated molecular docking applications (FRED, HYBRID, POSIT) and their associated workflows. This release features the official introduction of HYBRID, as well as a major upgrade to FRED.

POSIT - Ligand guided pose prediction FRED - Fast exhaustive docking HYBRID - Ligand guided docking

Reagents, This application details the structures and functions of >80 reagents encountered in typical introductory organic chemistry courses.

The 1Q KNIME newsletter is out. Discussion of text mining, the Feb UGM and Tips and Tricks.

http://knime.org/files/knimenewslettervol2no12012.pdf

KNIME (Konstanz Information Miner) is a user-friendly and comprehensive open-source data integration, processing, analysis, and exploration platform.

There is a KNIME tutorial here.

I’m not a Fortran user myself but I know a lot of scientists swear by it for high performance code, so I thought I’d mention Nocturnal Aviation Software the creators of FTranProjectBuilder the only Mac-native Fortran development environment (IDE) it works with the gfortran, g95, ifort, Absoft Pro Fortran, NAG nagfor and PGI pgfortran compilers.

FTranProjectBuilder is for scientists, engineers and students. It's useful for large, complex projects, but makes even simple programs easy to manage. To speed up program development it has:

• Single window interface
• Editor, console and notes views
• Project wide search
• Execution input from console or file
• Execution timer
• Errors and search results organized by file in outline view
• Add files by drag and drop, or import an existing makefile

FTranProjectBuilder manages the dependencies, object and module files, program executable and a standard makefile for you. You spend your time working on your code. FTranprojectBuilder does the rest.

Chem+ is a chemical reference for your iPad. Databases Include: * NIOSH Pocket Guide (NPG) * Immediately Dangerous to Life and Health (IDLH) * Toxicity (TOX) * the Emergency Response Guidebook (ERG)

Elemental from Dotmatics a Chemistry Sketch Utility

Elemental is the Dotmatics chemistry sketch utility provided at no charge within many Dotmatics products. Now provided as a FREE app on the iTunes store.

There is a list of mobile science apps here.

The latests marketshare data from NetApplications is available, and while there has been a small increase in the Mac desktop share over the year up to 6.53%, perhaps the more interesting feature is the steady rise of mobile browsing. Over the year there has been a 50% increase in the use of mobile devices (smartphones+tablets) from less than 5% to 7.3%. Much of this is driven by iOS which now accounts for 63% of the mobile market share.

Looking at the weblog for the Macinchem website the results are similar with iOS accounting for over 7% of the visitors, software vendors need to think about support for mobile platforms if they have not already.

In this screencast BioTeam shows how it can orchestrate an Accelrys Pipeline Pilot experiment running on a remote cloud (BT Compute) via Apple iOS Siri voice control.

In systems biology it is becoming a routine task to build models of increasing complexity on a given biochemical network or pathway of interest. One of the main problems in building such models is the determination of the parameters underlying each modelled process. ByoDyn has been designed to provide an easily extendable computational framework to estimate and analyse parameters in highly uncharacterised models

Just added to the alphabetical listing

Graphite - LifeExplorer is a tool for modelling DNA, the tool generates DNA along a Bézier curve, open or closed, allows fine-tuning of atoms' position and, most importantly, exports to PDB. This software allows to model in 3D assemblies of proteins and DNA. Its main feature is the capability to create 3D models of DNA in a highly intuitive manner. To date, the modeling and visualization tool allows to: - import PDB files - create isosurface of molecular object - highlight residues of interest - calculate distance between residues pairs - import and export in 3D formats - model DNA and export the result in PDB - visualize a 3D scene with Level of Detail - explore a scene with real-time ambient occlusion - import a file with x,y,z coordinates and convert it into a DNA representation.

You can see a it in action here

http://www.youtube.com/watch?feature=player_embedded&v=9db1hXZARoo

The award winning reference management application Papers has just been updated to version 2.2

• Recent papers search for Authors and Periodicals
• Auto-complete of authors and sources in the inspector
• Editing of multiple papers at once and duplicate merging of papers
• Merge and split any duplicate or incorrectly merged sources
• Displaying and navigation of notes and highlights in the inspector
• Addition of tools to allow page rotation and hiding a PDF coverpage
• Creating of collection hierarchies upon import of folders
• Return of column mode for search results in the search section
• Support for inserting footnotes in Microsoft Word
• Improved Papers for iOS syncing

The full list of new features are described here.

There is a list of reference management applications here.

Chemkit is an open-source C++ library for molecular modelling, cheminformatics, and molecular visualization.

DEVONthink has been updated, this maintenance release prepares DEVONthink Pro Office for the upcoming sync technology, introduces the new Activity panel, brings interface and usability enhancements, and fixes some minor bugs and glitches. It is recommended for all users of DEVONthink Pro Office.

DEVONthink Pro Office only:

• Improved: Compatibility to eastern European languages.
• Improved: Support for all versions of ExactScan.
• Improved: Threading of imported email messages.
• Fixed: Installation of Apple Mail plugin with ~/Library/Mail replaced with an alias or symbolic link.
• Fixed: Creator and producer attributes of OCRed PDF documents.
• Fixed: Size of date field of metadata entry window.

DEVONthink Pro and up:

• NEW: Script Add message(s) & attachments to DEVONthink for easily importing both messages and attachments.
• NEW: Support for categories of Atom feeds.
• Improved: Opening multiple databases uses now one progress indicator.
• Improved: Support for sheets, e.g. imported .csv files, with varying number of columns.
• Improved: Scripts > Import > Del.icio.us no longer uses the discontinued keychain scripting. In addition it is able to download and set a thumbnail for the group again.
• Improved: Encoding support for Add mailbox(es) to DEVONthink and Add message(s) to DEVONthink scripts.
• Improved: Automator action Set Current Group.
• Improved: Smart groups in the sidebar using the Date Opened condition are immediately updated.
• Improved: Handling of feeds not containing dates.
• Fixed: Issue preventing Sente 6 smart template from linking back to the original reference in Sente.
• Removed: Obsolete script Scripts > Feeds > Apple - Latest Mac OS X downloads.

DEVONthink Personal and up:

• NEW: Activity panel. Replaces the OCR Activity panel.
• NEW: Copy Frame Link contextual menu command for movies.
• Improved: Handling of Quick Look panel on OS X 10.6 Snow Leopard and later.
• Fixed: Two issues with tabbed document windows.
• Fixed: Crashes caused by Quick Look on OS X 10.8 Mountain Lion (workaround).
• Fixed: Dragging linked images from Safari stored them as bookmarks since the latest Safari updates.
• Fixed: Bookmarks to pages of PDF documents didn't always work on OS X 10.7 Lion.
• Fixed: Duplicate shortcuts in Format popup menu of Clip to DEVONthink panel.
• Fixed: Empty folders were not always deleted e.g. after deleting indexed items.

All editions:

• NEW: View option View > Columns > Aliases and sorting option View > Sorting > By Aliases.
• NEW: Number of items in groups , smart groups, and feeds is now displayed right aligned and gray.
• NEW: Creating new documents in Tags view adds them either to the currently selected group tag or to the inbox of the database and tags them with the currently selected (ordinary) tag(s).
• NEW: Double-clicking on entries in the Log panel reveals them or shows them in the Finder if possible.
• Improved: Data > See Also > Classify can now also be used when the drawer is already visible, e.g. to close it using the keyboard shortcut.
• Improved: Reliability when inserting links and attachments into rich text documents.
• Improved: Memory management.
• Improved: Overall reliability and performance.
• Fixed: Some minor user interface issues on OS X 10.7 Lion.
• Fixed: Smart groups using Item contains aliases were not always automatically updated.
• Fixed: Mouse cursor did not show as arrow over popup and clear buttons of search fields.
• Fixed: Reordering items in ordinary tags (inside the Tags group) wasn't possible in unsorted views.
• Fixed: Send by Email commands were not disabled if no documents were selected.
• Fixed: Using services or Clip to DEVONthink could cause issues while synchronizing with DEVONthink To Go.
• Fixed: Spotlight metadata cache didn't always contain all files.
• Fixed: Minor bugs and glitches.

There is a list of reference management applications here.

The latest beta test version of XQuartz has been released. Mac OS X 10.6.3 or later is required to install this package.

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

ASObjC Runner is an invaluable scriptable faceless background helper application. It has a dictionary with a range of commands focused on the areas where vanilla AppleScript comes up short. It adds the ability to use the power of Cocoa frameworks within Applescript.

You use it like a scripting addition, except you address the commands to the application. It provides better string handling (e.g. change case, encoding URL’s, regular expression, formatting dates), list sorting and filtering, improved file handling and progress dialog boxes.

I’ve added to the page of Applescript Resources

CFOUR (Coupled-Cluster techniques for Computational Chemistry) is a program package for performing high-level quantum chemical calculations on atoms and molecules. The major strength of the program suite is its rather sophisticated arsenal of high-level ab initio methods for the calculation of atomic and molecular properties. Virtually all approaches based on Møller-Plesset (MP) perturbation theory and the coupled-cluster approximation (CC) are available; most of these have complementary analytic derivative approaches within the package as well. Studies of excited electronic states and other "multireference" problems are possible using the equation-of-motion (EOM) coupled-cluster techniques. These techniques which are closely related to (and in some cases identical to) so-called Fock space multireference coupled-cluster theory, offer a powerful means to study open-shell systems and decided advantages when configuration mixing is important. At present, these include the EOMEE approach for singlet and triplet excited states, and the EOMIP and EOMEA methods that are best applied to low-spin doublet states. Analytic derivatives are available for these methods. A number of methodological developments have been added to the program in the last two decades. These include: analytic second derivatives for all coupled-cluster approaches up to full CCSDT; the calculation of NMR chemical shifts at MP and CC levels of theory; the calculation of anharmonic force fields (via numerical differentation of analytic derivatives); relativistic corrections; corrections to the Born-Oppenheimer approximation at the CC level; nonadiabatic coupling within the EOM framework, and several others.

It was recently announced that the Schrödinger Suite 2012 now supports Mac OS X, I don’t have many details other than those on the website. There is now a Mac OS X native version of Maestro 9.3, and PyMOL 1.5 supports Mac OSX 10.7, there is encrypted file transfer channel to clusters, including the Cloud (Linux and Mac only). There is also a Mac OS X native version of Canvas 1.5.

If anyone has more information please let me know.

Open Drug Discovery Teams (ODDT) is now available on the iTunes Store.

The idea behind ODDT is that there are many rare of neglected diseases that might benefit from collaborative efforts from scientists from multiple disciplines, ODDT is an application that supports informal interactions, provides a means to explore relevant information in a flipboard like interface in particular information tagged by other scientists with similar interests. The image below gives you an idea of the topics currently discussed.

This slideshow explains the genesis of the project, and how it has evolved.

So why not fire up iTunes and download the free app and get involved?

Just got this message I thought I’d pass on.

The iNMR reader will remain at €39 for another 5 days only. Staring from Tuesday, it will return to its old (historical) price of € 50. The same applies for the student promo and the laptop extensions, everything that now costs €39 will cost €50 starting from next Tuesday.

iNMR is the only NMR software expressly written for Mac OS X, it uses Mac technologies and is tightly integrated with Mac OS X.

There is a listing of spectroscopy applications here.

I just got sent this.

As part of BioMed Central's commitment to reproducible research and transparency in scientific communication, authors submitting manuscripts to some BioMed Central journals can obtain a complimentary subscription to LabArchives with an allotment of 100MB of storage. This account has all of the features of the Pro Version of LabArchives ELN with the exception of the storage allotment.

LabArchives apparently runs on all platforms including Mac there is also a free version with limited storage which I guess would be useful for trying it out.

Just updated the chemistry Safari extensions so they are compatible with the upcoming Safari 5.2.

http://matt-swain.com/post/20715501529/chemistry-safari-extensions-just-updated-the

It looks like the iPad is opening doors for Apple in the Biosciences.

There's mounting evidence that drug companies are changing the way they consume new tech, and one prime example of this shift is the industry's well-documented affection for Apple's iPad. Pharma companies are buying the tablets by the thousands, doling them out to sales reps and executives, some of whom probably already own the popular devices.

Read more: Pharma's iPad attraction marks tech adoption shift - FierceBiotechIT http://www.fiercebiotechit.com/story/pharmas-ipad-attraction-marks-tech-adoption-shift/2012-04-05#ixzz1rZGxpPVh

When the research firm asked more than 100 top life sciences companies about their plans for buying tech hardware in 2012, more than 30% of respondents expected to purchase Apple products, up 220% since 2009.

Read more: Apple emerges as 'dominant' life sciences IT player - FierceBiotechIT http://www.fiercebiotechit.com/story/apple-emerges-dominant-life-sciences-it-player/2012-04-03#ixzz1rZIGrYS1

JSDraw2 interface is changed a lot to fit the touch user experience: 1. The default button sizes are much bigger for fingers to touch 2. For smaller screen size, the toolbar buttons are smartly grouped and shrinked.  So even for phone screens, the JSDraw toobar is much easier to use 3. Zooming, moving, rotating and undo/redo gestures are fully implemented

Sdfchecker is a free inspection and manipulation program for SDFiles (.sdf). Summary of functions: - Indicate number of structure records - Indicate number of blank structure records - Display list of Data Field names - Remove blank structure records - Split large files into smaller multiple files, a single random sized file, or containing a specified range of records - Convert into individual MOL files - Inspect for duplicate Data Field names within each record

The Mobile Molecular DataSheet (MMDS) has been updated. Two major usability enhancements:

(1) Additional tool banks on the left and right side of the sketcher provide simplified drawing tools that are more familiar to users of desktop chemical drawing software.

(2) A tooltip system provides tips, live demonstrations and links to documentation.

Utopia Documents is an interesting PDF reader that has a number of useful features. It allows you browse through a publications images using a screen flow like display. It also provides links to online resources to enhance the document.

There is a listing of reference management applications here.

A new version of AMBER 12 and AMBER Tools 12 has been released, the main changes are:-

• Force fields: Amber has a new fixed-charge protein force field, ff12SB, enchanced support for polarizable potentials and a new modular lipid force field Lipid11 designed to be compatible with the other pairwise additive AMBER force fields.
• Expanded options for numerical Poisson-Boltzmann solvation calculations, including models for membrane systems and support for periodic systems.
• An enchanced 3D-RISM integral equation model, using the Kovalenko-Hirata (and other) closure approximations, with a better treatement of aqueous electrolytes.
• Improved ideas for self-guided Langevin dynamics and accelerated molecular dynamics, to enchance sampling along soft degrees of freedom.
• Simplified installation and automatic update support.
• Semi-empirical quantum calculations can use d-orbitals, allowing the use of Hamiltonian models such as AM1/d and PM6.
• QM/MM calculations can interface with a variety of external quantum chemistry programs, expanding the types of quantum models available.
• More features from sander have been added to the pmemd code for both CPU and GPU, including Temperature Replica Exchange, Isotropic Periodic Sum, Accelerated Molecular Dynamics and support for various harmonic restraints based on the use of NMRopt on GPUs.
• Expanded methods are available for free energy calculations that change Hamiltonian models, including better procedures for appearing and disappearing atoms, and tighter integration with replica-exchange simulations.
• New facilities are present for using electron density maps (e.g. from cryo EM/ET experiments) as constraints, and to support rigid (or partially flexible) groups in simulations.

There are detailed instructions for installing AMBER 12 under MacOSX and building CUDA enabled AMBER 12.

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

From the KNIME newsletter

“…good news for our Mac Users! We have just released KNIME 2.5.4 which fixes issues caused by the latest Apple update of the Java environment. We are grateful to the very active KNIME community which has helped to identify and fix this problem.”

KNIME Desktop 2.5.4 can be downloaded from the download page (http://www.knime.org/download) or you can upgrade your existing KNIME installation by using the built-in update functionality available in the "File" menu

There is also a KNIME tutorial here

Biscu-it™ is a collection of - hopefully - useful Python tools and functions that have been built on top of the RDKit chemoinformatics toolkit and that have been wrapped in a single Python package called Biscu-it™.

Virtual models for property Evaluation of chemicals within a Global Architecture (VEGA), Using the VEGA platform, you can access a series of QSAR (quantitative structure-activity relationship) models for regulatory purposes, or develop your own model for research purposes. QSAR models can be used to predict the property of a chemical compound, using information obtained from its structure. This version comes with some minor error fixes and with a new model (BCF Read-Across).

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.

SYBYL-X 2.0 release now available - with new Molecular Data Explorer, QSAR enhancements, and updates for Surflex-Sim and Surflex-Dock to make performing your CADD modeling studies more intuitive and efficient.   

The Molecular Data Explorer is a multi-component tool for molecular data analysis and visualization, and early testers tell us they obtain insights into their dataset in minutes that previously would have taken days.

I was reminded that whilst scripting menu items was the traditional way of controlling ChemDraw the more recent releases allow control by scripting commands. This is a major advance since menus can change or be translated into other languages. I’ve thus updated the script.

I was asked if it would be possible to do the same thing for other drawing packages such as MarvinSketch?

The answer is yes but because MarvinSketch does not have applescript support we have to do it slightly differently. Rather than using scripting commands we script system events to evoke the “Paste” command.

Full details of the script are here

SPRESImobile provides direct access to ChemReact, a subset of the SPRESI structure and reaction database, which contains more than 400,000 unique reaction types and the related references. SPRESImobile allows searching by name and structure queries, exact, substructure and All-in-one (Flex) search. There is a list of iOS applications on the mobile science page.

The name to structure feature in ChemBioDraw is very useful but is pretty much limited to systematic names and certainly does not support other chemical identifiers like CAS Numbers. There are a number of online services that do support these sort of functions but you end up having to cut and paste from different web sites. This is where the Chemical Identifier Resolver script comes into play.

POSIT is primarily based on the assumption that similar ligands bind similarly. Unlike most docking protocols, POSIT requires the presence of a known bound ligand. The bound ligand is used to impart docking constraints when placing and optimizing the geometry of the molecule being docked.

Equalizer is the standard middleware to create and deploy parallel OpenGL-based applications. It enables applications to benefit from multiple graphics cards, processors and computers to scale the rendering performance, visual quality and display size. An Equalizer application runs unmodified on any visualization system, from a simple workstation to large scale graphics clusters, multi-GPU workstations and Virtual Reality installations. Equalizer 1.2 is a feature release extending the 1.0 API, distilling seven years of development and decades of experience into a feature-rich, high-performance and mature parallel rendering framework and an object-oriented high-level network library. It is intended for all application developers creating parallel, interactive OpenGL applications. Equalizer 1.2 can be retrieved by downloading the source code or one of the precompiled packages.

There is an interesting publication in Journal of Cheminformatics 2012, 4:7 doi:10.1186/1758-2946-4-7 describing CheS-Mapper .

CheS-Mapper (Chemical Space Mapper) is a 3D-viewer for chemical datasets with small compounds.
It can be used to analyze the relationship between the structure of chemical compounds, their physicochemical properties, and biological or toxic effects. CheS-Mapper divides large datasets into clusters of similar compounds and consequently arranges them in 3D space, such that their spatial proximity reflects their similarity.

I’ve been doing a little work to update iBabel, I’ve updated all the tools developed by Silicos-it to use the new names and options.

The SVG support in Openbabel has undergone significant improvements due to the brilliant efforts of Noel O’Boyle and Chris Morley in particular the ability to colour a substructure within a molecule. This requires installation of the development version of OpenBabel at present.

I’ve added a movie to show it in action.

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.

One of the critical activities of most drug discovery programs is the identification of novel leads, these hits can come from high throughput screening or fragment-based screening There is however great interest in virtual screening which allows the evaluation in silico of a vast number of compounds and the selection of a subset that have a greater chance of desired activity. The virtual screening can be achieved by searching using sub-structures or molecular descriptors, by docking potential ligands into the target protein and scoring the resulting docked pose, or by comparing with the shape and/or electrostatic map of a known ligand.

Shape-it is a tool developed by Silicos-it that aligns a reference molecule against a set of database molecules using the shape of the molecules as the align criterion. It is based on the use of Gaussian volumes as descriptor for molecular shape as it was introduced by Grant, J.A.; Gallardo, M.A.; Pickup, B.T. (1996) ‘A fast method of molecular shape comparison: a simple application of a Gaussian description of molecular shape’,J. Comp. Chem. 17, 1653-1666.

This script shows how to run shape-it from within Vortex, bringing in the shape matching scores for filtering and analysis.

Open3DALIGN is a command-line molecular alignment tool which is operated by means of a few commands which can be entered interactively from a command prompt, read from a batch script or piped through standard input. If PyMOL is installed on the system while Open3DALIGN is being operated interactively, the setup of alignments can be followed in real time on PyMOL's viewport.

Open3DGRID is an open-source software aimed at high-throughput generation of molecular interaction fields (MIFs). Open3DGRID can generate steric potential, electron density and MM/QM electrostatic potential fields; furthermore, it can import GRIDKONT binary files produced by GRID and CoMFA/CoMSIA fields (exported from SYBYL with the aid of a small SPL script).

Open3DQSAR is an open-source tool aimed at pharmacophore exploration by high-throughput chemometric analysis of molecular interaction fields (MIFs). Open3DQSAR can generate steric potential, electron density and MM/QM electrostatic potential fields.

MolSoft have announced the release of ICM version 3.7-2c.

New features include Atomic Property Fields APF is a 3D pharmacophoric potential implemented on a grid. APF can be generated from one or multiple ligands and seven properties are assigned from empiric physico-chemical components (hydrogen bond donors, acceptors, Sp2 hybridization, lipophilicity, size, electropositive/negative and charge).

The 3D ligand Editor is a powerful new tool for the interactive design of new lead compounds in 3D. It allows you to make modifications to the ligand and see the affect of the modification on the ligand binding energy and interaction with the receptor.

Use AQUASITES to design chemicals based on their ability to displace or keep water molecules inside the ligand binding site of proteins. The first step is to identify water binding sites and then the second step is to estimate the free energy of water displacement for a particular ligand(s).

Protein Modelling Inside ICM there are many features for homology modelling and loop modelling. This new option can be used if you have a gap in your protein and you want to find loops in the PDB which fit the gap.

"Pipe-able" Scripting in ICM. New options to pipe icm commands and scripts. Easy way to write pipe-able scripts (see $ICMHOME/molpipe/*.icm). Easy way to add parallelism to unix/mac ICM scripts: fork with pipe option ($ICMHOME\molpipe*.icm)

Absoft Corporation, today announced general availability of a new Xcode 4.3 Compatibility Pack for Absoft Pro Fortran 2012 customers running Mac OS X. The Compatibility Pack is available (only) as part of Absoft's new Service Pack v11.5.1 for Pro Fortran 2012 Mac OS customers.

The Compatibility Pack allows installation of Pro Fortran 2012 with Xcode 4.3 and is compatible with Apple's reorganized directory structure.

The Service Pack v11.5.1 which includes the Compatibility Pack for Mac OS X can be downloaded at NO CHARGE by current Absoft Pro Fortran 2012 Mac OS X customers from:http://www.absoft.com/download/downloads.html

For additional details contact: sales@absoft.com or www.absoft.com

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 Brain Lab to the list of mobile science applications Brain Lab is a brain cell simulator, currently it offers

1. A passive integrate and fire model
2. A full Hodgkin-Huxley model with sodium and potassium channels
3. A Library to learn more about brain science

Brain Lab offers real scientific brain cell models that can be used by anyone, no matter if you are a student, a scientist, or someone who is just interested in brain science. To carry out your experiments, they have set up a Lab for you with all the necessary equipment. If you need to brush up your brain science knowledge or look up a specific technical term, you can go to your Library and read it up. 

UCSF Chimera is a highly extensible, interactive molecular graphics program is available for MacOSX, both X-windows and native versions are available. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics

This is a major update and whilst some of the new features and tools are described below full details can be found at http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.6.html#1.6. Note this will be the last release supporting Mac PowerPC platforms.

New Tools:

• Animation (Utilities) under development, not fully functional, may change significantly — save/restore Chimera scenes
• Cage Builder (Higher-Order Structure) — create polyhedral cages composed of hexagons, pentagons, and other polygons
• Change Chain IDs (Structure Editing)
• MultiFit (Volume Data) — simultaneous rigid fitting of multiple structures into density (uses RBVI web server running the program MultiFit from the Sali lab)
• Palette Editor (Utilities) — create and choose palettes (series of colors and interpolation method; currently used for background color gradients)

• Renumber Residues (Structure Editing)

  New Commands:

• background — set background color(s) or image

• changechains — reassign chain IDs
• fitmap — command implementation of Fit in Map, plus features not available in that tool:
• global search with random initial placement
• sequential fitting of multiple different structures
• symmetric fitting of copies of the same structure
• invert — swap substituents
• resrenumber — renumber residues
• ibclass — set ribbon residue class: which atoms control ribbon path and which are hidden by ribbon
• ribspline — set ribbon path method: B-spline or cardinal spline; control additional smoothing and “stiffness” of cardinal spline ribbon
• scene — save and restore scenes, which include positions, display status and styles, labels, etc. (see also new tool: Animation)
• zonesel — select atoms and/or surfaces within a cutoff distance of specified atoms and/or surfaces (this command allows defining zones by surfaces, whereas the standard command-line zone operators < and > refer to atoms only)

The latest data from Net Applications is in, Mac OS X is up to around 7% whilst Windows is now down to just below 92%.

iOS continues to dominate the mobile/tablet market (60%), with Android (19%) and Java ME (14%) being the only others in to double figures.

The Open Drug Discovery Teams (ODDT) project is a mobile app primarily intended as a research topic aggregator of open science data integrated from various sources on the internet. It exists to facilitate interdisciplinary teamwork and to relieve the user from data overload. Initial research topics include areas of chemistry and adjacent molecule-oriented biomedical sciences, with an emphasis on those which are most amenable to open research at present. The ODDT project uses a free mobile app for iOS-based devices (iPhone, iPod and iPad) as the hub. The app has a Flipboard-inspired interface, and serverside infrastructure for hosting data and value added services. The project is open to participation from anyone, and much of the content is derived from public sources but is amenable to commercial data input and they are now looking for alpha testers. One of the key components is a back-end server that is in charge of monitoring the appearance of tweets with certain hash tags (#tuberculosis, #malaria, #hivaids, #huntingtons, #sanfilipposyndrome and #greenchemistry).

There is a screencast here to give you an idea of the functionality.

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.

I just got this message.

I am pleased to announce the release of the program RESP ESP charge Derive version III.5 (or R.E.D. III.5) and its related tools (Ante_R.E.D.-1.5 and X R.E.D. III.5) available @ http://q4md-forcefieldtools.org/RED/. New features available: - Bug corrections and code cleaning, - Update of the Mini-HowTo & Tutorials, - Better handling of Gaussian, GAMESS and Firefly error messages, - Charge value rounding off errors automatically corrected at 10-6 up to 10-2 depending on the user choice, - Handling geometrical constraints in the P2N file format (geometry optimization using the Gaussian program), - Two new scripts for data submission in R.E.DD.B., - New version for the RESP program: version 2.2 with updated documentation. The R.E.D. III.5 tools are distributed under the GNU General Public License after a simple Register & Download procedure. The article describing the R.E.D. tools is available @ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/. News about the latest developments of R.E.D. IV can be found @ http://q4md-forcefieldtools.org/RED/popup/news.php. Best regards, The q4md force field tools team

R.E.D. allows computational biologists involved in AMBER/GAFF, CHARMM, GLYCAM & OPLS force field based biological studies to automatically derive highly effective and reproducible charge values, and to build force field libraries for new molecules and molecular fragments.

A couple of people have contacted me about the news that X11will not part of the standard distribution of the next version of the Mac operating system. X11 is a key UNIX windowing system for a number scientific applications and I can understand the concern. However whilst X11 has been included in the past it should be noted that the distributed version is simply a snapshot of XQuartz, in the future this will be automatically downloaded.

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. It may in fact be better if users download the latest version of XQuartz when needed since they provide regular updates which are unfortunately overwritten when you install a Mac OS update.

Indeed the team have already provided a latest development version that is compatible with Mountain Lion (XQuartz  2.7.1 rc4 - 2012.02.11), if you find any bugs or issues I urge you to report them to the XQuartz team !

I’ve mentioned Silicos-it in the past and I thought I’d highlight them again since they have had a major makeover, the website has moved and the tools have been updated and renamed.

Silicos-it has contributed it’s expertise to the chemoinformatics community by porting its source code into the open source domain. Examples include the spectrophore descriptors, the filtering program filter-it and the pharmacophore tool align-it.

Command-line tools

Filter-it™ is a command-line program for filtering molecules with unwanted properties out of a set of molecules. The program comes with a number of pre-programmed molecular properties that can be used for filtering.

I used the filter-it (previously called Sieve) in a Vortex script, I’ve rewritten the script and the tutorial to account for the name change.

Strip-it™ is a tool to extract molecular scaffolds according predefined rules. These rules are based on the definitions of scaffolds as described by Bemis & Murcko (J. Med. Chem. 1996, 39, 2887), Pollock (J. Chem. Inf. Model. 2008, 48, 1304) and Schuffenhauer (J. Chem. Inf. Model. 2007, 47, 47).

Align-it™ is a pharmacophore-based tool to align small molecules. The tool is based on the concept of modeling pharmacophoric features by Gaussian 3D volumes instead of the more common point or sphere representations. The smooth nature of these continuous functions has a beneficent effect on the optimisation problem introduced during alignment.

Shape-it™ is a shape-based alignment tool by representing molecules as a set of atomic Gaussians. The software is based on the method described by Grant and Pickup (J. Phys. Chem. 1995, 99, 3503).

Spectrophores are one-dimensional descriptors generated from the property fields surrounding the molecules. This technology allows the accurate description of molecules in terms of their surface properties or fields. Comparison of molecules’ property fields provides a robust structure-independent method of aligning actives from different chemical classes. When applied to molecules such as ligands and drugs, Spectrophores can be used as powerful molecular descriptors in the fields of chemoinformatics, virtual screening, and QSAR modeling. The Spectrophore code was developed by Silicos, and donated to the OpenBabel project in July 2010.

I just thought I’d mention that Journal of Computer-Aided Molecular Design commissioned some Perspectives on the state and future of the field to commemorate the journal's 25th anniversary and have made this content open access for a limited period.

Special Issue: The next 25 years: Commemorating the 25th anniversary of the Journal of Computer-Aided Molecular Design

There are some very interesting insights, well worth reading.

Edit

Have a read of Alpha shock by Mark A. Murcko • W. Patrick Walters

Sanjay toggled the telepresence feature on his iPhone (standard since IOS 27.2) and he and Paolo were instantly ‘‘together’’ examining a set of images from the virtual pharmacology study.

OMEGA v2.4.6 has been released. This is a major release with new features including an extension to the MMFF94 force field for three coordinated boron compounds. Designed for use with the large libraries required for computer-aided drug design, OMEGA rapidly generates multi-conformer structure databases.

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.

I’ve added two new applications from Metamolecular to the alphabetical listing.

ChemVector™ offers a modern solution to the chemical structure imaging problem. Features

• 100% JavaScript. No browser plugins are necessary.
• Runs with all commonly-used browsers on Windows, Linux, Mac, and iPad. This includes Internet Explorer 6-9 in addition to Firefox, Google Chrome, and Safari.
• Renders structures directly from individual molfiles on a server, or as inline content.
• Renders chemical structure content directly from ChemDraw™ binary files (.cdx).
• Declarative syntax replaces <img> tags with analogous <object> tags, making it easy for both developers and designers to work with the resulting markup.
• Non-blocking implementation makes it possible to render dozens of structures on a single page while maintaining UI responsiveness.
• Structures can be magnified pre- or post-rendering with no pixelation.

ChemCore is the chemiformatics foundation of all of the Metamolecular products and services. Written in Java and cross-compilable to a number of target runtimes and platforms, ChemCore is both fast and flexible.

Features

• Fast subgraph matching
• Powerful graph query capabilities
• Flexible, efficient graph traversals
• Fast file input/output
• A complete system of atomic weights and elemental properties
• Sensible handling of implicit hydrogens
• Molecule validation and correctness-checking
• Molecule transformations, including canonicalization and salt-stripping
• 100% Java cross-compilable to JavaScript and other target runtimes and platforms
• Extensively tested and documented

A great tip from Dan at Dotmatics, if you want to know how your website might look on an iPhone/iPad use the iOS Simulator in the developers tools.

I was reading the announcements of new products from OpenEye and I thought I should update the listings.

AFITT from OpenEye is the only software to offer a fully automatic ligand fitting process that optimizes a real-space fit to density while keeping conformational strain to a minimum. It capitalizes on a combination of core technologies that OpenEye has developed, specifically conformer generation, shape potential, high quality small molecule structure minimization, and visualization. The key step, after finding the appropriate conformers and aligning them to density, is the implementation of a refinement that combines force field and shape potentials, via a series of adiabatic optimizations [1]. The AFITT distribution includes both a GUI and a collection of command-line applications.

BROOD is a software application designed to help project teams in drug discovery explore chemical and property space around their hit or lead molecule. BROOD generates analogs of the lead by replacing selected fragments in the molecule with fragments that have similar shape and electrostatics, yet with selectively modified molecular properties. BROOD fragment searching has multiple applications, including lead-hopping, side-chain enumeration, patent breaking, fragment merging, property manipulation, and patent protection by SAR expansion.

FILTER is a very fast molecular filtering and selection application. It uses a combination of physical property calculations and functional group knowledge to remove undesirable compounds before they enter experimental or virtual screening. Undesirable properties may include: toxic functionalities, a high likelihood of binding covalently with the target protein, interfering with the experimental assay, and/or a low probability of oral bioavailability.

QUACPAC provides pKa and tautomer enumeration in order to get correct protonation states. It also offers multiple partial charge models (including MMFF94 [1], AM1-BCC [2], and AMBER [3]) that cover a range of speed and quality in order to allow appropriate charging for every end use. QUACPAC's approach to tautomeric enumeration is to provide multiple tautomeric states rather than one "correct" tautomer. Subsequent downstream processes are then used to identify the appropriate tautomeric form.

SZYBKI optimizes molecular structures with the Merck Molecular Force Field, either with or without solvent effect, to yield quality 3D molecular structures for use as input to other programs. Since the chemistry of molecular interactions is a matter of shape and electrostatics, it is impossible to consider either without reasonable 3D molecular structures. SZYBKI also refines portions of a protein structure and optimize ligands within a protein active site, making it useful in conjunction with docking programs.

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!

There have been a few comments about an older blog posting concerning EBioTools so I thought I’d bump it to the top of the list.

EBioTools is a compilation of bioinformatics software that has been packaged for easy installation on Mac OS X. It covers many areas, from simple sequence analysis to RNA folding and sequence assembly.

The included software is:

• Name Version
• Boost1.3.41
• Clustal W1.83.UNIX
• PHYLIP3.6b
• EMBOSS5.0.0
• EMBOSS.kaptain0.98
• gd2.0.35
• Glimmer3.02
• HMMER2.3.2
• INFERNAL0.7
• Jmol11.2.12
• Kalign2
• Kaptain0.72
• MrBayes3.1.2
• MRSr482
• MUSCLE3.6
• NCBI Tools2.2.16
• NEdit5.5
• Primer31.1.2
• sim42003-09-21
• soap4r1.5.8
• Staden1.7.0
• T-COFFEE5.05
• ViennaRNA1.6.5

As mentioned in the comments added to the older post “EBioTools works under Snow Leopard and Lion but Staden is broken because Apple changed several Libraries to make the MacOSX core "smaller". Most issues are due to Apple changing graphic libraries.”

Users might also be interested in eBioX which brings easy-to-use sequence analysis to Mac-using biologists. It features an editor for sequences and multiple alignments, and graphical viewers for trace files and molecule structures. Many popular file formats are supported. Databases can be created locally or queried over the network, both for metadata and homology (BLAST). Analysis functions include searching for patterns, primers, restriction sites and repeats, translation and back translation, calculating DNA melting temperature, dot plots, as well as aligning sequences (multiple, local and global). Multiple alignments can be created by several of the most popular algorithms

In December the DOE Office of Advanced Scientific Computing Research (ASCR) published a report on Cloud Computing for Science. The key findings were

• Cloud approaches provide many advantages, including customized environments that enable users to bring their own software stack and try out new computing environments without significant adminis- tration overhead, the ability to quickly surge resources to address larger problems, and the advantages that come from increased economies of scale. Virtualization is the primary strategy of providing these capabilities. Our experience working with application scientists using the cloud demonstrated the power of virtualization to enable fully customized environments and flexible resource management, and their potential value to scientists.
• Cloud computing can require significant initial effort and skills in order to port applications to these new models. This is also true for some of the emerging programming models used in cloud computing. Scientists should consider this upfront investment in any economic analysis when deciding whether to move to the cloud.
• Significant gaps and challenges exist in the areas of managing virtual environments, workflows, data, cyber-security, and others. Further research and development is needed to ensure that scientists can easily and effectively harness the capabilities exposed with these new computing models. This would include tools to simplify using cloud environments, improvements to open-source clouds software stacks, providing base images that help bootstrap users while allowing them flexibility to customize these stacks, investigation of new security techniques and approaches, and enhancements to MapReduce models to better fit scientific data and workflows. In addition, there are opportunities in exploring ways to enable these capabilities in traditional HPC platforms, thus combining the flexibility of cloud models with the performance of HPC systems.
• The key economic benefit of clouds comes from the consolidation of resources across a broad community, which results in higher utilization, economies of scale, and operational efficiency. Existing DOE centers already achieve many of the benefits of cloud computing since these centers consolidate computing across multiple program offices, deploy at large scales, and continuously refine and improve operational efficiency. Cost analysis shows that DOE centers are cost competitive, typically 3–7x less expensive, when compared to commercial cloud providers. Because the commercial sector constantly innovates, DOE labs and centers should continue to benchmark their computing cost against public clouds to ensure they are providing a competitive service.

Eagle Genomics have a nice summary, that addresses many of the highlighted issues.

QuantumBio Inc. have announced the release of Version 5.1.1 of its DivCon Discovery Suite which includes support for the newest version of the Molecular Operating Environment (MOE) platform from Chemical Computing Group, Inc.

MOE/DivCon GUI is an integration interface that joins the QBLib with the powerful Molecular Operating Environment (MOE) from the Chemical Computing Group (CCG), creating a technological innovation for protein/ligand scoring (energetically favorable), featuring QM, PWD, and NMR Scores.

The update also includes:-

• MOE/DivCon: For pairwise energy decomposition heatmap, sequence alignment within the MOE/DivCon interface has been completely overhauled in order to use CCG's sequence alignment tool.
• MOE/DivCon: Multitasking within the MOE/DivCon graphical user interface runs freely while DivCon is running in the background. Improved QM convergence reporting to MOE's svl window.
• File Processing: Included HDFView and QBReporter applications for opening and processing *.h5 output files, and translating them to Excel or OpenOffice spreadsheet files. Reported results include QMScores, partial charges, gradients, and significant events. QBReporter requires that OpenOffice 3.3.0 or greater from OpenOffice.org has been installed and that the resulting soffice executable is available within the command line $PATH.
• Core: Support for Sun Grid Engine (SGE) in addition to the Portable Batch System (PBS). Note: SGE requires that its parallel environment (PE) be activated in order to run multiprocessing jobs.
• Core: Shipment of both 32bit and 64bit native versions of all Linux binaries in order to account for larger memory, disk, etc (and therefore larger target/ligand structures).
• Core: Separation of QuantumBio-specific software from 3rd party binaries (such as mpirun) in order to allow for parallel installations of the same.
• MOE/DivCon: Inclusion of ${QBHOME}/bin/qbmoe and ${QBHOME}/bin/qbmoebatch to run system-installed MOE and MOE/batch with QuantumBio-required options.
• MOE/DivCon: Addition of support for MS Windows7 (64bit) both for preparation and analysis. Prepared structures can then be characterized with qbmoebatch on Linux or Mac OS X.
• Documentation: Completely updated on-line documentation for MOE/DivCon.
• MOE/DivCon: Entirely redesigned and streamlined dialogs, and improved integration with standard MOE structure preparation and analysis tools.
• MOE/DivCon: Patented QMScore integrated as an available score function for MOE tools including Dock, Scaffold Replacement, BREED, etc.
• DivCon: Support for additional input file formats including cif, sdf, and h5.
• DivCon: Command line --help switch improved to provide default settings, simplified

iFormulas is a clean, simple, easy to use mathematical formula reference guide. Formulas : Algebra, Calculus, Chemistry, Geometry and Trigonometry. Over 380 formulas, definitions, laws, properties, etc.

MyCalculator is an innovative 2D and 3D graphing calculator featuring One Touch Graphing™ and an innovative memory system to store and recall answers. Just touch the answer bar to store numbers in multiple memory slots.

MathStudio, formerly SpaceTime, is the most comprehensive math app available for iPhone and iPad. Whether you need a simple calculator to do your finances or a replacement for your TI graphing calculator,

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.

The 'AppleScriptObjC Explored' Addenda and Errata page has been updated to cover a change made in Xcode since version 4.0 came out. <http://www.macosxautomation.com/applescript/apps/errata.html>

AppleScriptObjC Explorer v2.2 is now available. It's a free update to existing users, and incorporates all the changes in the last beta version, plus built-in updating.

Myriad Helpers 1.0.2 is now available. It's a minor update, offering a new method fordTrig: to give access to trigonometry functions. <http:www.macosxautomation.com/applescript/apps/helpers.html>

I just got this message:-

We are pleased to announce the official release of Q-Chem 4.0.  Q-Chem 4.0 represents the latest development in quantum chemistry methodology and includes:

• Dispersion-corrected and double hybrid DFT functionals;
• Faster algorithms for DFT, HF and coupled-cluster calculations;
• Structures and vibrations of excited states with TD-DFT;
• Methods for mapping complicated potential energy surfaces;
• Efficient valence space models for strong correlation;
• More choices for excited states, solvation and charge-transfer;
• Effective Fragment Potential and QM/MM for large systems;
• Shared-memory for multicores and implementations for GPU's.

A complete list of the new features can be found at the our website: http://www.q-chem.com.

The updates to two of major packages for computational chemistry have been announced

NWChem 6.1 has been released with the latest Global Arrays Toolkit (GA-5.1). Full details of the update can be found here.

SCM has announced the 2012 release of its suite of chemical modelling programs: ADF, BAND, DFTB, MOPAC, ReaxFF, and COSMO-RS. Full details of the update can be found here.

MolPrime is a chemical structure drawing tool based on the unique sketcher from the Mobile Molecular DataSheet

Added to the Mobile Science Page.

The January market share data is out from Net Applications.

The desktop share is dominated by Widows (92%) and Mac OSX (6.4%), interestingly nearly 50% of the Windows machines are still operating XP.

The remorseless rise in the use of mobile platforms continues with mobile/tablet browsing now up to 8.8% an increase of over 1% over last month and more than 100% over the year. iOS continues to dominate (53.6%) with Java (19%) and Android (18%) juggling for second place. Blackberry is now down to 2.6% and falling rapidly.

This might be of interest.

Dotmatics is looking to expand the team working on Vortex, its data analysis platform. The candidate should have several years software development experience with Java and preferably with the Swing graphical user interface toolkit. The ideal candidate will have a degree or PhD in the life sciences, and will have experience with data visualisation and analysis techniques such as clustering. Experience with cheminformatics systems or statistical software, such as R, will be advantageous. Candidates will probably have experience working within the pharmaceutical/biotech sector or the life science software development industry.

The position will be based at the UK headquarters in Bishops Stortford (Herts, UK). We offer a competitive salary, benefits and a pleasant working environment at the Old Monastery site. Further information about the company and our software can be found at http://www.dotmatics.com.

Over the years I’ve migrated from Applescript Studio applications to AppleScriptObjC using Xcode 3 and last week I made the transition to Mac OSX 10.7.x and Xcode 4. With each transition there has been a very steep learning curve and to be honest the documentation provided by Apple has been woefully inadequate. Thankfully Shane Stanley has stepped up to the plate and provided a definitive guide for this people who want to build applications using applescript. AppleScriptObjC Explored is the definitive guide to building AppleScript Objective-C applications. It guides you step-by-step through the process of integrating the power of Cocoa into your AppleScript applets and applications, demonstrating each concept and technique in fully editable and annotated example projects.

The latest edition also includes a detailed navigation of Xcode 4, for those of us who had just learnt our way around Xcode 3 the changes made in the new version are significant and the section explaining where everything is and what they are for is invaluable, in fact it is probably worth reading this section before you start trying to write your first application.

Once you have a basic understanding of Xcode adding an interface to your script becomes largely point and click.

There is also a very useful section on trouble-shooting, and explanation of “gotchas” that will crop up occasionally.

The book comes with a collection of over 20 ready built Xcode tutorials/projects that demonstrate key implementations but that can also act as starting points for your own projects.

Whilst I keep a list of applescript resources, I suspect that AppleScriptObjC Explored is probably the most useful.

ORCA is a modern electronic structure program package has been updated

New Features

1) The parallelization of the program is now completed. All modules, including MRCI, are now parallel. Parallel performance has been improved in numerous cases. 

2) A new module for performing efficient spin adpted single excitation configuration interaction calculations for open shell systems (ROCIS). This is particularly powerful for the calculation of transition metal L-edge X-ray absorption spectra. It is parallelized

3) A new module performing molecular dynamics calculations with ORCA. Also available for methods that only feature numerical gradients. 

4) MDCI module: • Orbital optimized coupled cluster version for RHF and UHF (also parallelized) • Brückner coupled cluster (including triples) for RHF and UHF • SEIO functional for orbital invariant, stationary coupled pair calculations • Open shell LPNO-CEPA,QCISD and CCSD methods • Parameterized CCSD (pCCSD) in canonical and LPNO versions (RHF and UHF)

5) CASSCF: • Relativistic CASSCF for the variational treatment of spin orbit coupling. Also uses symmetry. • Projection SOC states on spin-free states possible • Kramers restricted RELCAS • Numerous improvements in NEVPT2 (COSMO, Trajectories and scans, Direct-RI modeless storage) • Improved convergence and convergence aids (... but we are still working on this) • Spin-Spin coupling in QDPT CASSCF/NEVPT2 for magnetic properties • Determinant based full CI program added for the CI step

6) MRCI • Fully parallelized including the QDPT procedure for magnetic properties

7) General/Misc. improvements • VDW10. Latest dispersion correction from the group of Grimme • Nonlocal DFT-NL for incorporation of dispersion in DFT • PW6 B95, PWP B95, RI-PWP B95 functionals • Rappoport/Furche optimized basis sets for properties • Basis set extrapolation now works also with def2 basis sets • Densities for interactive orcaplot • Differences and transition densities in orcaplot • Natural orbitals for unrelaxed MP2 density • SOS-MP2, SOS-RI-MP2, SOS-OO-RI-MP2 energies + gradients • DKH picture change for g-tensors • Overlap fitted RIJCOSX procedure leads to further speedups and improvements in accuracy • Libint2 for more efficient integral evaluation (uses contraction) • Parallelization of point charge correction for QM/MM • Interface to the MRCC program by Mihály Kállay

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

Reference Miner searches the Internet to find and display reference information from PubMed, Amazon (US, UK, Germany, France, Canada, Japan, Italy, and China), Google Scholar, JSTOR (requires access privileges and ip authentication) and the Library of Congress. The Internet search features of Reference Miner, and much more, are built into Bookends. If you own Bookends you do not need Reference Miner.

There is a list of reference management applications here.

Chemical Drawing Programs – The Comparison of Accelrys (Symyx) Draw, ChemDraw, DrawIt, ACD/ChemSketch, ChemDoodle and Chemistry 4-D Draw

http://dragon.unideb.hu/~gundat/rajzprogramok/dprog.html

There is also a comparison of six chemical drawing packages 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

PTHPasteboard is comprehensive clipboard manager that supports multiple text and image clipboards, these can then be accessed via a customisable icon in the menu bar or from a floating window, clicking on an item in the clipboard history displays the application that the data was copied from and for text items shows the number of lines/words/characters and for images the size. PTHPasteboard also supports filtering of clipboard text allowing you to convert to unformatted text, convert to lower/upper case, change to Mac/Unix/Windows line endings. There is also a custom filter dialog that allows you to build your own filters for example to convert a list from a text document into an html list. It also allows the creation of custom clipboards. PTHPasteboard PRO's Syncing support takes advantage of Mac OS X's Bonjour technology to seamlessly sync your pasteboard items across multiple machines.

I’ve been using it for a couple of weeks now and I thought I’d share few tips.

There is a new update to Bookends (11.2.4 )

• Updated Google Scholar direct search and Autocomplete Paper to deal with changes made by Google
• Import abstracts from Google Scholar Note that the abstracts Google Scholar provides are incomplete, but still may be helpful.
• Type ahead search works in the single column reference list The search is always for the author, regardless of the sort status of the list. It will only jump to an exact match of the typed characters.

There is a comprehensive list of reference management software here.

I was just catching up with some reading and I came across an article in Algorithms for molecular biology describing ViennaRNA 2.0 consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. With the new release of version 2.0, they introduce the most recent nearest neighbour energy model for all free energy calculations. Additionally, most of the stand-alone programs included are now able to read FASTA formatted input data. The distribution includes:-

• RNAfold -- predict minimum energy secondary structures and pair probabilities
• RNAeval -- evaluate energy of RNA secondary structures
• RNAheat -- calculate the specific heat (melting curve) of an RNA sequence
• RNAinverse -- inverse fold (design) sequences with predefined structure
• RNAdistance -- compare secondary structures
• RNApdist -- compare base pair probabilities
• RNAsubopt -- complete suboptimal folding
• RNAplot -- RNA structure drawings in PostScript, SVG, or GML
• RNAcofold -- predict hybrid structure of two sequences
• RNAduplex -- predict possible hybridization sites between two sequences
• RNAup -- predict RNA-RNA interaction sites using accessibilities
• RNAalifold -- predict the consensus structure of several aligned sequences
• RNAaliduplex -- comparative (multiple alignment) version of RNAduplex
• RNALfold -- predict locally stable structure of long sequences
• RNAplfold -- compute average pair probabilities for local base pairs in long sequences
• RNApaln -- fast structural alignment of RNA sequences using string alignments
• Several small but helpful Perl Utilities

According to the authors both 1.8.x and 2.0 versions of the Vienna package compile and run on Mac OS X. Currently there's a small compile problem with the included Perl module and the latest gcc versions on Intel based Macs. The defaults for gcc recently changed to compile only Intel code, while the installed Perl is a fat binary containing both PPC and Intel code. The download page contains instruction how to work around this by simply setting an environment variable.

I just heard about a platform - FORECASTER - that includes programs for drug discovery and process chemistry, these include

1. FITTED, a docking program
2. PREPARE, PROCESS and SMART, programs that can prepare protein and ligand files automatically
3. CONVERT, a program that converts 2D molecules to energy-minimized 3D molecules (adds hydrogens, generates tautomers and protomers)
4. SELECT, a program that computes compound similarity, extracts focused highly diverse libraries or identifies analogues
5. REDUCE, a program that filters using descriptors and functionnal groups
6. REACT, a program that performs combinatorial chemistry in silico from user-defined chemical schemes
7. IMPACTS, a sites of metabolism prediction program (CYP 450)
8. ACE, a program that predicts the stereochemical outcome of reactions

All the programs are integrated into a new web-based graphical interface that allows complete automation of the different workflows. 

You can read more details here, Integrating Medicinal Chemistry, Organic/Combinatorial Chemistry, and Computational Chemistry for the Discovery of Selective Estrogen Receptor Modulators with Forecaster, a Novel Platform for Drug Discovery

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.

After many months of beta testing the latest version of the popular Mac dedicated NMR spectroscopy application iNMR5 has been released. The key new features are tabulated below.

• 64-bit
• Version 5 requires a 64-bit Intel chip and Snow Leopard. Version 4 is 32-bit Universal Binary and requires Tiger.
• real-time dragging
• When you drag the margins of the plot, or the integrals, or most of the objects, the plot is continuously updated. Overlay manager
• The Overlay Manager becomes non-modal and can be enlarged to show the full path of the individual documents. Sorting the overlays is simpler and more transparent.
• Manual phase correction
• The zero-order correction is controlled by a knob that never reaches the end of the run. The fine-coarse selector has many more stops. The phase panel is more compact.
• Other dialogs
• “Units and Scales” and “Colors and Levels” change the corresponding plots as soon as you click into a control. The Preferences dialog includes a “Preview” button. The color panel is no more modal. When the open dialog is open, the corresponding menu item isn't dimmed anymore. The console is more compact than in the past, but can be enlarged at will.
• Fit to overlay
• Fitting a simulated spin system is visibly faster.
• Cursors
• The new cursors are more specific. The horizontal palette has a single row of buttons.
• Info tool
• The interpolator is faster, more predictable and more reliable.
• Animation
• The visual effect of the command ”New Page” is realistic.
• Printing
• The printed area is no more centered and no more clipped.
• Tabulator
• Shows an estimate of the T1.

Depending on your existing license you may be eligible for a free upgrade, for other users there is a small upgrade fee.

There is a list of spectroscopy applications for the Mac 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 just got a note that MacVector has been updated to version 12.5 MacVector is a comprehensive Macintosh application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, and a variety of other functions. MacVector is widely regarded as the most intuitive, easy to use program available for sequence analysis.

For many years I’ve used the excellent Clipboardsharing to exchange the clipboard contents between my laptop and desktop machines, it also supports multiple clipboards. However it is not supported under Mac OS X 10.7.x (Lion) and the developer website seems to have disappeared. I spent a while looking at various alternatives and I thought I’d summarise my findings.

I should add I had a pretty clear view on my needs.

• Exchange clipboard contents (text and images) between laptop and desktop machines running Lion
• Have multiple clipboards
• Ability modify text e.g. remove formatting

Nice to have

• Keyboard shortcuts
• Option to encrypt clipboard contents before transfer
• Also exchange clipboard contents with iOS devices

Clipboard Evolved

Clipboard Evolved features a clipboard-like window for managing clips, a menu bar icon, and now a cover-flow interface for quickly pasting clips. It supports both text and images, and Clipboard Evolved has eight "complex" animation options to choose from: Ripple, Copy Machine, Star Burst, Irregular Holes, Disintegrate, Swipe, Crystallize, and Dissolve. It does not support clipboard sharing.

ClipMenu

ClipMenu is a clipboard manager that supports a number of text and images types including Plain text, Rich Text Format (RTF), Rich Text Format Directory (RTFD), PDF, Filenames, URL, TIFF image, PICT image. The clipboard history can then be accessed via an icon in the menu bar or via a shortcut key. ClipMenu can manage re-usable text as snippet. You can select it from menu and paste it anytime. It does not support clipboard sharing.

Clips

Clips automatically generates and arranges copied items into Application-specific clipboards, these can then be accessed via a Finder like interface or via an icon in the menu bar. It also supports live search so you don’t have to scroll through them, just start typing in the Clips Board or Organizer and non-matching items will fly off the screen instantly. It does not support clipboard sharing.

Clyppan

Clyppan is a clipboard history application that keeps a list of text you have copied to the clipboard, these can then be accessed via an icon in the menu bar. Clyppan only supports text clippings, but the history is searchable and pressing the spacebar will give you a Quick Look-style preview of the clipping, it also does not support clipboard sharing.

CopyLess

CopyLess supports all data types supported by the Mac OS X clipboard and has inline searching and Quicklook integration to allow you to check what you are pasting, it also keeps track of the application the data was copied from. It does not support clipboard sharing.

CopyPaste Pro

CopyPaste Pro is a popular clipboard history tool that can then be accessed via an icon in the menu bar or a graphical browser, CopyPaste Pro also has a selection of clipboard tools that allow the user to manipulate the data on the clipboard. It also allows the creation of archives to store clips for later use. It does not support clipboard sharing.

CuteClips3

CuteClips 3 is a recent update, it supports text and images which can then be selected from a list. It supports shortcuts and has an extensive list of keyboard shortcuts for manipulating the list and pasting options. It does not support clipboard sharing.

iClip

iClip supports copying plain-text, rich-text, images, audio, video, or files and all can be accessed in a rather neat iClip dock that sits on the side of the screen, you either drag and drop to and from the iClip history bins or copy and paste. It is possible to preview images in clip bins which might be very useful if you are working a lot of the time with images. It supports keyboard shortcuts, but does not have clipboard sharing.

Jumpcut

Jumpcut is an open source application that provides multiple clipboards. Every time you copy some text it is added to the Jumpcut stack, these can then be accessed via a scissors icon in the menu bar. Alternatively you can view the list via a hot-key. It does not however support images and as far as I can tell no plans for clipboard sharing.

PTHPasteboard Pro 4

PTHPasteboard is comprehensive clipboard manager that supports multiple text and image clipboards, these can then be accessed via a customisable icon in the menu bar or from a floating window, clicking on an item in the clipboard history displays the application that the data was copied from and for text items shows the number of lines/words/characters and for images the size. PTHPasteboard also supports filtering of clipboard text allowing you to convert to unformatted text, convert to lower/upper case, change to Mac/Unix/Windows line endings. There is also a custom filter dialog that allows you to build your own filters for example to convert a list from a text document into an html list. It also allows the creation of custom clipboards. PTHPasteboard PRO's Syncing support takes advantage of Mac OS X's Bonjour technology to seamlessly sync your pasteboard items across multiple machines.

Savvy Clipboard

Savvy Clipboard holds a list of items that you copied — text fragments, graphics, URLs, multimedia data, or links to files — and lets you access them using this list from either a floating window or menu bar icon. You just select the needed item from the list, and it is ready to use from the system Clipboard, so you can paste it anywhere you want. While it is possible to export a list and transfer to another computer it does not support clipboard sharing.

ShadowClipboard

ShadowClipboard is another fairly comprehensive application, with unlimited clipboard sets, clipboard sharing, clipboard filtering and clipboard set backups, the clipboard history can then be accessed via an icon in the menu bar or from a window. It supports keyboard shortcuts, and shadowClipboard uses Apple's ZeroConf networking called Rendezvous. shadowClipboard clients will automatically recognise each other on a local network.

Stuf 2

Stuf 2 has a different way to share clipboards in that Stuf stores your clippings and can share them with any other Stuf users, even in a different country, with your permission of course. Stuf can use any network drive to share clippings, but they really recommend you use DropBox. Stuf 2 is available for both Mac and PC. It supports text and images and clipboard history can then be accessed via an icon in the menu bar.

So I bought PTHPasteboard which best meets my needs but obviously your needs may vary. There are also a couple of clipboard sharing tools Syncopy, which is nice because it supports Mac OS X and iOS, CrossClip which works between Mac, Linux and PC.

The migration of the site is now complete, and I think all the missing images, incorrect formatting, broken links etc. are now fixed, many thanks to all those who reported problems.

I’ve been adding Google Analytics to pages so I have a better idea of what is popular and to get a better view of the readership. It is early days yet but it looks like the site is getting 15 - 20, 000 hits a month, with around 70% being new visitors to the site. The average time spent on the site is 4 mins which would suggest most find content that they want to read. As you might expect 70% of the visitors are using Mac OS X, 20% Windows but interestingly 5.5% are now using an iPad. In fact >95% of the visitors using a mobile device are using iOS. Nearly 40% of the visitors from the US and 15% from the UK, the remaining european countries contribute a couple of percent each as do Japan, India, China and Australia there was even one visitor from Trinidad and Tobago who spent 4 minutes browsing the site.

The top search terms are iBabel, emolecules, chemical drawing, atom modelling knime and tutorial.

The most popular pages are the blog, mobile science, the reviews, data analysis tools and applescript.

The RSS feed and Twitter feed seem to be picking up new readers each week.

I’ll look again in six months and see how things have progressed

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.

I’m just catching up with things that happened over the last month or so and I noticed that the reference management application Papers has been updated to version 2.1.

If you want to know what features are currently being developed for future versions of Papers have a look at the roadmap.

There is a list of reference management applications here.

Chirys Draw is an innovative, best-in-class application for drawing publication-quality molecular structures and reactions. Designed from the ground up for the iPad, Chirys Draw takes advantage of unique multi-touch capabilities to make drawing molecular structures and reactions easy and accurate. Chirys™ Sketch is an innovative, best-in-class application for drawing publication-quality molecular structures and reactions. Designed and built from Chirys Draw, the iPad version, Chirys Sketch takes advantage of unique multi-touch capabilities to make drawing molecular structures easy and accurate.

There are many more applications on the mobile science page.

CMol is a molecular viewer designed specifically for the iPad, iPhone and iPod touch, offering a more powerful system for displaying and understanding biological molecules than has yet been seen on any iOS device.

There are many more applications on the mobile science page.