Macs in Chemistry

Insanely Great Science

bioinformatics

Creating a Bioconda recipe

 

A little while back I mentioned BioConda. You can read more details in this publication "Bioconda: A sustainable and comprehensive software distribution for the life sciences", DOI. Conda is a platform- and language-independent package manager that sports easy distribution, installation and version management of software.

The conda package manager has recently made installing software a vastly more streamlined process. Conda is a combination of other package managers you may have encountered, such as pip, CPAN, CRAN, Bioconductor, apt-get, and homebrew. Conda is both language- and OS-agnostic, and can be used to install C/C++, Fortran, Go, R, Python, Java etc

The bioconda channel is a Conda channel providing bioinformatics related packages for Linux and Mac OS. Looking through the packages it is clear there it already contains a number of chemistry packages. These include: Updated 24 November 2017

  • OpenBabel
  • Rdkit
  • Opsin
  • chemfp
  • gromacs
  • osra
  • Autodock Vina
  • openmg
  • align-it
  • strip-it
  • shape-it
  • np-likeness-scorer
  • PubChem.py
  • Smina

Bioconda offers a collection of over 3100 software tools, which are continuously maintained, updated, and extended by a growing global community of more than 330 contributors. Rather than try to duplicate this effort for a "Chemconda" it seems more efficient to encourage chemists to contribute to Bioconda. If you do package a chemistry application for Bioconda please let me know and I'll publicise it on my blog and add it to the list above. To start things rolling I've added PubChem.py to Bioconda and I've written a page describing how to create a bioconda recipe.

Link to page Creating a Bioconda recipe



Comments

Bioconda: A sustainable and comprehensive software distribution for the life sciences

 

Bioconda is a channel for the conda package manager specializing in bioinformatics software.

Bioconda supports only 64-bit Linux and Mac OSX.

Bioconda offers a collection of over 2900 software tools, which are continuously maintained, updated, and extended by a growing global community of more than 250 contributors. Bioconda improves analysis reproducibility by allowing users to define isolated environments with defined software versions, all of which are easily installed and managed without administrative privileges.

The conda package manager has recently made installing software a vastly more streamlined process. Conda is a combination of other package managers you may have encountered, such as pip, CPAN, CRAN, Bioconductor, apt-get, and homebrew. Conda is both language- and OS-agnostic, and can be used to install C/C++, Fortran, Go, R, Python, Java etc

You can read more details in this publication "Bioconda: A sustainable and comprehensive software distribution for the life sciences", doi.

Whilst there are a number of compilaions of Bioinformatics software, Bioconda looks to be by far the most comprehensive.

After installing Conda, the first step is to set up the Bioconda channel

conda config --add channels conda-forge
conda config --add channels bioconda

Packages can then be installed using

conda install cnvkit

This installs CNVkit plus the appropriate Python and R dependencies.


Comments

New HELM web-editor

 

Just got this message..

The HELM project team is happy to announce the release of an open source web-editor to complement it's existing suite of software. This web-editor is designed to support organisations that do not wish to deploy a thick client. This is an initial release and the functionality will be extended in further releases during 2017.

HELM Web Editor brings HELM’s industry standard biomolecular representation to the browser, greatly enhancing the deployability of the technology for its adopters

Current functionality includes:

  • HELM 1 support
  • The ability to use the supplied monomer libraries to draw macromolecules, visualise them as sequences or atom/bond structures and calculate properties.
  • Import/export of HELM and xHELM.
  • A limited set of rules that allow you to manipulate the structure.

screenshot1


Comments

Scientific Applications under Sierra (Update 14)

 

Whilst there are many sites that track the compatibility on common desktop applications, it is often difficult to find out information about scientific applications. I’ll update the list regularly and feel free to send in information.

When I compiled a similar lists for Yosemite and El Capitan they proved very popular with 13,000 page views, I hope this page is similarly useful.

4Peaks no reported issues

Avogadro all seems OK

BBEdit version 11.6.2 and newer are compatible, recommend against using earlier versions

Brainsight requires version 2.3.3 for full compatibility with 10.12 Sierra. You could note too that 2.0 through 2.2.x will never work because 10.12 removed support for garbage collected applications. 2.3.x uses ARC

ChemDraw the official line is that it is not supported, even under El Capitan there were reports of copy/paste issues. One user reports “ChemDraw 15 is working fine for me. copy/paste, everything without issues”.

ChemDoodle no reported issues

CrystalMaker “We are pleased to confirm that all our latest software runs fine on macOS “Sierra”, as well as OS X 10.11 “El Capitan”, 10.10 “Yosemite”, and earlier.”

CYLview app launcher (icon on the desktop or the dock) does not work need to start using “Terminal”

DataDesk Data Desk 8 for Mac runs on OS X 10.7 up to 10.12

DataWarrior requires Java installation

DEVONagent has been updated to version 3.9.5 to support Sierra, in addition this update brings support for Qwant. DEVONthink has also been updated for Sierra.

EndNote From Endnote (Thomson Reuters) version 7: Message for Mac user planning to update to Sierra: In preparation for Apple's release of macOS Sierra on September 20, we have been testing various versions of EndNote. Through our testing, we discovered some issues with the EndNote PDF viewer. These issues have been reported to Apple, but in the meantime, we recommend that you DO NOT upgrade to macOS Sierra.

EnzymeX no reported issues

Evernote a bug in some versions of Evernote for Mac that can cause images and other attachments to be deleted from a note under specific conditions. We've released an updated version of Evernote for Mac, version 6.9.1, to resolve this.

Findings no reported issues

Fortran users will be happy to hear there are no reported issues with FTranProjectBuilder

GAMESS no reported issues.

Homebrew, after every update it is worth checking your homebrew installation.

Username$ brew doctor
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry and just ignore them. Thanks!

Warning: /usr/local is not writable.

You should probably change the ownership and permissions of /usr/local
back to your user account.
  sudo chown -R $(whoami) /usr/local

Warning: /usr/local is not writable.
Even if this directory was writable when you installed Homebrew, other
software may change permissions on this directory. For example, upgrading
to OS X El Capitan has been known to do this. Some versions of the
"InstantOn" component of Airfoil or running Cocktail cleanup/optimizations
are known to do this as well.

You should probably change the ownership and permissions of /usr/local
back to your user account.
sudo chown -R $(whoami) /usr/local

Once corrected you can then type

brew update
brew upgrade

You may get this error

$brew update
/usr/local/Library/brew.sh: line 32: /usr/local/Library/ENV/scm/git: No such file or directory

simply retyping brew update seems to resolve the issue

If you have previously installed Openbabel using

brew install mcs07/cheminformatics/open-babel --HEAD

The "--HEAD" part means install the latest development version from GitHub. The latest version of OpenBabel is now available so type

brew uninstall mcs07/cheminformatics/open-babel
Uninstalling /usr/local/Cellar/open-babel/HEAD... (309 files, 14.6M)
brew install mcs07/cheminformatics/open-babel

You can check you have the latest version installed by type this in a Terminal window

obabel -V
Open Babel 2.4.0 -- Sep 24 2016 -- 14:01:18

iBabel seems to work fine with the latest version of OpenBabel under Sierra. One advantage to updating to OpenBabel 2.4.0 is that previews now work with Quicklook.

quicklook

IDL does run under Sierra but does require some tuning. Detailed instructions here

iPython Notebook all working fine

Lego Mindstorms At the moment everything seems to be running really great on Sierra. However, please let you readers know they are welcome to contact us via the website way you did if they run into any errors. We'd be happy to solve them!

Manuscripts no reported issues

MarvinSketch I had to reinstall Java for Mac OSX this is the last version of Java Apple created to support legacy applications, similarly MarvinSpace and MarvinView.

Matlab in general appears to be fine except for certain language localisations these languages a patch is available for download. A patch is also available for MATLAB Runtime R2016b.

Mathematica 11.0.1 has been compatibility tested with macOS Sierra and you should not run into any OS-specific compatibility issues. The font-panel is disabled, but we are actively working to address this as soon as possible.

Mendeley no issues reported

MOE working fine, XQuartz did not need reinstalling. However the MOE app launcher (icon on the desktop or the dock) does not work because Apple changed some fundamental system components which affects lots of programs not specifically compiled for the newest MacOSXs. Also you cannot double click on a file to open it in MOE. You can still start MOE from the command line

Applications/moe2015/bin/MOE

It then works perfectly. Update, just had an email from CCG support, The problem with the MOE app launcher on MacOSX Sierra has been fixed in the MOE 2016 release.

MOPAC all seems to be working fine.

osra crashed with error abort trap: 6. I uninstalled using brew then reinstalled

brew uninstall osra
Uninstalling /usr/local/Cellar/osra/2.0.1... (7 files, 1.6M)
brew install osra

Then worked fine

Pandoc depends on llvm-3.5, not supported on Sierra. Llvm-3.9 is supported, installation using Homebrew seems to be OK.

Papers Mac 3.4.7 (527) is now available! Fixes a couple of problems under Sierra. A crash that can occur when switching PDFs, The search in PDF functionality is restored

R latest version (3.3.1) all seems fine

rdkit installed using home-brew works fine.

Readcube Version 2.22.13732 is Mac OS Sierra (v10.12) compatibility update.

Scansnap Note for using ScanSnap or ScanSnap Applications on macOS Sierra In order to avoid the ScanSnap compatibility problems, please do not use ScanSnap or ScanSnap applications on macOS Sierra in the following manner as doing so may cause some pages to be deleted or to become blank. Do not use [ScanSnap Organizer], [ScanSnap Merge Pages], or [CardMinder] Do not use Excellent mode when scanning A3 (11.7 in. x 16.5 in.) documents No image data will be lost nor any blank pages produced when content that has been scanned in the A4 (8.3 in. x 11.7 in.), Letter (8.5 in. x 11 in.), Legal (8.5 in. x 14 in.), or smaller sizes is saved.

Schrodinger a reader sent in this response. We received your query regarding MacOS Sierra. Unfortunately our current, 2016-3 release, do not yet support MacOS Sierra but we have plans to include support for this OS for the upcoming 2016-4 release of our software.

SeeSAR version 5.3 now, 5.4 will come out shortly. No compatibility issues observed/reported.

Studies no reported issues

UCSF Chimera version 1.11.1 seems to be working fine

Wizard worked great with the developer pre-releases, no reported issues

Vortex no problems so far, the embedded chemical drawing app Elemental appears to have no issues.

XQuartz did not require reinstallation :-) however there are reports of an intermittent display not found error when launching apps from a Linux box.

Allow applications downloaded from anywhere in macOS Sierra, if you open the security panel in the Settings the default options in Sierra are as shown below. There is no longer the option to open applications from Anywhere.

appstore

Apple have removed this function on macOS Sierra, but you can re-enable it running this in terminal

sudo spctl --master-disable

appstore2

You can restore it back to the default setting using

sudo spctl --master-enable

I’ll add more updates later.


Comments

Vortex does Biology

 

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

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

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

sequaligned

Added to the growing list of software reviews.


Comments

ICM version 3.8-5

 

MolSoft have announced the release of ICM version 3.8-5.

  • Generate a 2D Interaction Diagram of a ligand with the binding pocket. The image is annotated with hydrogen bonds and interacting residues.
  • 3D ligand editor is a powerful tool for the interactive design of new lead compounds in 3D
  • ICMJS is a JavaScript/HTML5 viewer for 3D Molecular Graphics which does not require any plugin or installation.
  • Support for MMTF format. The Macromolecular Transmission Format (MMTF)
  • Support for Mac retina display
  • Add docking restraints by selecting atoms in the receptor
  • Updates to protein modelling, bioinformatics and cheminformatics

Full release notes are here


Comments

BioExcel: An Introduction

 

An overview of the BioExcel Project.

BioExcel is based on improving three aspects of biomolecular research. Firstly, improving the performance and scalability of the most commonly used software, such as GROMACS (www.gromacs.org), HADDOCK (www.haddocking.org) and CPMD (www.cpmd.org), to take advantage of next-gen HPC systems and the expected increase in the amount of data produced. It’s also important to improve how easy it is for users to access and use these types of software. Not all researchers have experience in efficiently handling data and software. BioExcel aims to provide customisable workflow environments, which will allow relatively novice HPC/HTC users take advantage of the analysis software provided in ways that suit their specific research. In addition to this, hands-on training and public webinars are already underway, aiming to teach researchers best practices and how to best utilise the software and resources available.


Comments

Cytoscape Update

 

Cytoscape has been updated to version 3.4.0

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

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


Comments

BALL Project

 

BALL (Biochemical ALgorithms Library) is an application framework implemented in C++ that has been specifically designed to reduce development times in the field of Computational Molecular Biology and Molecular Modeling. It provides an extensive set of data structures as well as classes for Molecular Mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, and visualization.

BALLView is BALL’s standalone molecular modelling and visualization application. Furthermore, it is also a framework for developing molecular visualization functionality.

BALLView_01

It can be downloaded from here and requires

  • CMake >= 2.8.12
  • git
  • Python 2.7
  • Qt 5.4

Installation instructions for Mac OSX are here


Comments

Uniprot Feature Viewer

 

Data analysis tools are becoming ever more important as the volume of data increases and I thought I'd flag a new resource Feature viewer

A new visual approach by UniProt, the universal protein resource, presents protein sequence features in one compact view using a highly interactive BioJS component. This is the first visualisation feature in a public resource that lets users see different types of protein sequence features such as domains, sites, PTMs and natural variants from multiple sources in a single view.

featureviewer


Comments

HELM integration with RDKit

 

The Pistoia Alliance HELM project have announced free MarvinBeans 5.0 licenses and integration of HELM with the RDKit cheminformatics suite.

The Pistoia Alliance HELM project has made two major announcements that help cement the reputation of HELM as the de-facto standard for describing and working with complex macromolecular structures. Firstly, HELM users can now take advantage of free MarvinBeans 5.0 licenses for the HELM toolkit. Secondly, RDKit is now HELM-enabled, making it a valuable addition to the extensive range of open source HELM-enabled tools.

Comments

Protein-Ligand Interaction Profiler has been updated

 

The PLIP Protein-Ligand Interaction Profiler has been updated.

According to the Changelog

1.2.0

  • Support for DNA and RNA as ligands__
  • Detection of metal complexes with proteins/ligands, including prediction of geometry__
  • Extended result files with detailed information on binding site residues and unpaired atoms__
  • Support for zipped and gzipped files__
  • Rich verbose mode in command line with information on detected functional groups and interactions
  • Automatic fixing of common errors in custom PDB files
  • Refined binding site selection
  • Better overall performance
  • Initial test suite for metal coordination
  • Classification of ligands
  • Improves detection of aromatic rings and interactions involving aromatic rings
  • Single nucleotides and ions not excluded anymore as ligands
  • Generation of canonical smiles for complete (composite) ligands
  • Generation of txt files is now optional
  • Basic support for PDBQT files
  • Correct handling of negative chain positions of ligands
  • Improved check for valid PDB IDs
  • Fixes several bug

The web service includes all the updates and integrates BioLip for flagging biologically relevant interactions. Since ligand molecules (e.g., Glycerol, Ethylene glycol) are often used as additives (i.e., false positives) for solving the protein structures, not all ligands present in the PDB database are biologically relevant.

Comments

Polyphony

 

Polyphony is an open source software suite written in python. Its purpose is the superimposition free analysis and comparison of multiple 3D structures of the same or closely related protein molecules.

Absolute Requirements

python 2.6 or later, scipy, numpy, Biopython, especially the Bio.PDB module

Highly recommended

All following documentation assumes that you have these installed.

ipython , for interactive python scripting, matplotlib, for graph plotting, PyMOL, for interactive 3D visualisation. Open source version available on SourceForge

William R Pitt, Rinaldo W Montalvão and Tom L Blundell, BMC Bioinformatics, 2014, 15:324 doi

Comments

Workshop on Resources for Computational Drug Discovery

 

I just thought I'd mention this upcoming workshop, as ever there is a top class line up.

EMBL-EBI/Wellcome Trust Workshop on Resources for Computational Drug Discovery 2-6 November 2015 Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

https://registration.hinxton.wellcome.ac.uk/display_info.asp?id=510

The draft agenda is here

Comments

BioTuple Open Beta

 

iChemLabs the developers of ChemDoodle the very popular chemical drawing application have just announced the open beta of a new product BioTuple.

If you are looking for a bioinformatics system that encompasses all the aspects your workflow in one program, BioTuple™ is the solution for you. BioTuple works on all operating systems (both 32 and 64 bit), allows for easy importing and exporting to common biological file types, and keeps all the functions you would want organized into views. This allow you to easily switch between running an alignment, visualizing restriction sites and more in one cohesive interface

biotuplemainslider2

Objectives

  • Clean and clear graphics representations of sequences that are dynamic and responsive to keyboard and mouse input.
  • Quickly and easily import sequences from external databases such as NCBI and RCSB.
  • Visualization of features either manually or computer assisted for small and large sequences.
  • Highly customizable parameters for pairwise and multiple sequence alignments.
  • Alignment reports including phylogenetic trees, statistics, and consensus comparisons.
  • Clear visualization of all reading frames for RNA and DNA sequences.
  • Viewing of content analyses and properties of a given sequence.
  • Visualize the 3D structure of a sequence using PDB files imported from the RCSB.

As I mentioned this is an open beta and thus offers a unique opportunity to have an input into the design of the software, so please let your friends, colleagues and students know that this tool is available to them.

You can sign up for beta testing here: http://www.biotuple.com/beta-signup.


Comments

MacVector 14 released

 

A new version of MacVector has been released, the updated is now a 64-bit application meaning that it can take full advantage of all of the memory installed on your computer, allowing it to handle larger sequences and alignments. MacVector14 is no longer dependent on the deprecated “CarbonLib” compatibility library. This helps ensure that MacVector will continue to work with future releases of OS X where this library is likely to be removed.

Bowtie has been updated to support version 2 which can handle gaps in the aligned reads. This allows the use of much longer input reads (which typically have more indels) and provides far more accurate coverage information because, with the older version, reads with indel mismatches would be discarded even if they were "real" matches. The Primer Design (Primer3) “Test” mode now has a text output similar to the old Test PCR Primer Pair functionality, allowing you to view details of all of the possible products generated by the pair of primers. There are some cool new "Rounded Rectangle" feature graphics types. You can now directly select residues in the Map view in the default "zoom" mode. This lefts you use the Map tab for all editing operations except for actually typing residues (but you can select then click on the Editor tab to do that). MacVector now supports the new Regulatory GenBank feature type. You can import features into a sequence with files formatted using the Sequin Table format. More options in the way the sequence Editor and Map views are initialized are now saved to preferences so that MacVector “remembers” how you like to view your sequences. The cut sites and recognition sequences of restriction enzymes and now listed in the text outputs. Colored residues or background in the single sequence Editor tab are now only displayed if the underlying feature is located on the sequence line. This provides much finer control over which regions of the sequence you would like to see highlighted in color.

Comments

Protein-Ligand Interaction Profiler

 

Whilst this is not a Mac application I thought I'd mention it since it seems a very nice implementation.

The Protein-Ligand Interaction Profiler (PLIP) is a web service and command line tool for fully automated characterization of non-covalent interactions between proteins and ligands in 3D structures.

You can either upload a PDB format file or use the search facility to use a PDB by protein, ligand or enzyme-commission number. You can combine multiple search terms to be more specific (AND search).

I used the PDB code 3EQB, the software correctly identified two ligands, ATP and the more interesting ligand CHEMBL485945.

You can view the results using the embedded 3D molecule viewer JSmol shown in the image below.

plip1

PLIP is based on a python command-line application. In case you plan local mass/batch processing, you may want to use this one directly. The source code can be found on PLIP on Git Hub.

I first tried this out on my desktop machine and it worked beautifully, I then tried it out on my iPad and iPhone and the website functioned exactly as expected.

Comments

Unipro UGENE

 

I've just been sent details of a free open-source bioinformatics package Unipro UGENE first described in Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 2012 28: 1166-1167. doi:10.1093/bioinformatics/bts091. Commercial support is also available.

3dstruct

Comments

Differ

 

Differ is an ultra-fast yet easy-to-use tool to browse, search, split and combine VCFs

Opening a 1.5 GB VCF file in a text editor can take a while, even on modern computers. Differ opens these VCFs in a second or two on any modern Mac (best with SSD).

Differ requires Mac OS X 10.10

Comments

Scientific Applications under Yosemite (Update 12)

 

Whilst there are many sites that track the compatibility on common desktop applications, it is often difficult to find out information about scientific applications. Given that this seems to be such a major upgrade I thought I’d set up a spare machine to test applications before I update my main machine. I’ll update the list regularly and feel free to send in information.

I have a number of applications/libraries/toolkits installed using Homebrew and installed in usr/local, this is known to cause extended installation times for Yosemite. So don’t worry if it appears the install is stuck at 1 min remaining.

If you do use Homebrew then it is worth updating

brew update
brew upgrade

Aabel 3 appears to be working fine

BBEdit version 10.5.13 and newer are compatible with Yosemite

Beaker all seems OK

ChemBioDraw versions 12, 13 and 14 all function as before.

ChemDoodle all seems to work fine

Chimera aka UCSF Chimera versions 1.10 and higher are working on Yosemite.

Conquest and  Mercury from CCDC works fine but you may need to reinstall Quartz (see below)

Cresset report that after testing that Torch, Spark, Forge and Blaze appear to be compatible with Yosemite, the only cosmetic issues are due to a couple of as yet unresolved bugs in QT here.

Cytoscape 3.1.1 seems to be working fine

DataWarrior no issues

EndNote X7.2 works well with Yosemite.

Findings Electronic Notebook no issues, only small issue is that the ‘+’ button of the window does not trigger full-screen, though it can still be done via the Window menu.

IDL 8.2 and earlier gags on a missing reference in libPng.dyld, but IDL 8.3 and later is OK

Igor Pro version 6.3.5.5 works fine

iNMR no problems reported

MacVector 13.0.6 No significant issues reported

Marvin Marvin, Instant JChem, and JChem suite all work but require Java 7 (available here http://support.apple.com/kb/DL1572

Mathematica no issues reported

Matlab 2014b works fine, 2012a thru 2014a need patching (directions available from Mathworks support site. Older versions will not run at all..

MOE works fine but you may need to reinstall Quartz (see below)

OpenBabel no issues so far

Opsin all works fine

OSRA no issues

Papers Current version is compatible but not optimised, they hope to have a beta out of a substantially redesigned version next week.

Pro Fit 6.2 appears to work fine.

Pybel no issues reported

PyCharm works fine

Pymol All these are confirmed to work:

  • MacPyMOL 1.7.2.3
  • MacPyMOLX11Hybrid 1.7.2.3 after XQuartz reinstall (see below)
  • Open-Source PyMOL with homebrew

Known issues with MacPyMOL: - Movie export broken. Edu-only-PyMOL (free Student version) Does not work.(Now updated to work with Yosemite)
No reports so far about about - Other legacy versions (0.99 etc.) Apparently progam will not open - Open-Source PyMOL with fink or macports

PyRx 0.8 for docking works fine

RDkit no issues reported

SeeSAR all seems to be working fine

Sente 6.7.8 seems to run fine, except that it cannot open a reference library from the File > Open... dialog box. Workaround is to open from Finder.

Spartan 14 does not work because the Sentinel drivers are broken in Yosemite. The problem is NOT with Spartan, it is with the SafeNet developed Sentinel Run-Time Environment driver (the license manager). SafeNet has not given a definitive date when they will release an updated driver with Yosemite compatibility, but they are working on this. Best advice is to not upgrade but if you have to then contact support@wavefun.com for a temporary alternative license procedure.

Torch no issues

VarSeq no issues

Vortex Upgraded when the developer preview came out.  All works fine

The VVI products work well enough on Yosemite, but I'd like to achieve a higher level of quality for Yosemite (and iOS/iPad). There is an ongoing beta program for this product: https://itunes.apple.com/us/app/graph-ide/id904733611?mt=8 which is Graph Builder reincarnated on the iPad. There is also a beta program ramping for Graph Builder on Yosemite: https://itunes.apple.com/us/app/graph-builder/id470597599?mt=12 but a last minute interaction bug with Yosemite has delayed that for perhaps a few days. Please feel free to broadcast this information as you see fit. Beta program participation should be directed to support@vvi.com

VMD no issues reported

Wizard Pro is fully Yosemite compatible

XQuartz it seems the Yosemite installer deleted the symlink between /opt/X11 and /usr/X11; you can either reinstall Quartz or try "ln -s /opt/X11 /usr/X11"

Updated 30 October 2014

Comments

Biology Applications for MacOSX

 

I’ve been asked if I could include some biology/bioinformatics tools in the alphabetical listing, and I’m happy to add any that are sent to me, this week I’ve added.

CellDesigner

Cytoscape 3.1.1

GenomeBrowse

VarSeq

Comments

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

 

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

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

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

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

Comments

CLC Chemistry Workbench updated

 

The CLC Drug Discovery Workbench has been updated to version 1.5.

The new features are described on the updates page and in a video.

Comments

EnzymeX Updated

 

The Apple Design Award winning application EnzymeX has been updated. EnzymeX is a beautifully designed DNA sequence editor that Comes with numerous helpful tools and calculators, and includes handy reference data like codon tables and amino acid tables.

mapping

Talking to the developers they have fixed some 10.8/10.9 bugs, added gatekeeper support, and then reviewed the entire enzyme list and made quite a lot of changes as things had been updated throughout the years. In the process adding about 100 new enzymes, there is now Restriction enzyme information for almost 700 commercially available enzymes

Comments

Learning Python

 

It seems that Python is becoming the preferred language for scripting in science and I wrote a getting started page for Chemists and several people have pointed out a couple of resources that may be useful in particular Roaslind.

Rosalind is a platform for learning bioinformatics and programming through problem solving.

I looks like an excellent starting point for newcomers and more experienced programmers, whilst focussed on bioinformatics the exercises are useful for all disciplines.

For chemists chempython looks to be a very useful resource.

Comments

Chem-Path-Tracker

 

There is an interesting publication in the latest issue of Chemical Biology and Drug Design describing, Chem-Path-Tracker An automated tool to analyze chemical motifs in molecular structures DOI. This is a plugin for the molecular visualisation tool VMD that allows the user to highlight and reveal potential chemical motifs with a protein using only a few selections.

bindingsite

The chemical motifs can be a small group of residues or structure protein fragments with highly conserved properties that have important biological functions. However, the detection of chemical motifs is rather difficult because they often consist of a set of amino acid residues separated by long, variable regions, and they only come together to form a functional group when the protein is folded into its three dimensional structure. Furthermore, the assemblage of these residues is often dependent on non-covalent interactions among the constituent amino acids that are difficult to detect or visualize. To simplify the analysis of these chemical motifs and give access to a generalized use for all users, we developed Chem-Path-Tracker.

More details on the project page

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RCSB mobile PDB viewer

 

The official PDB viewer has been updated

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Amber 14 and Amber 14 Tools released

 

Version 14 of the Amber software suite has been released (There was no "unlucky" Amber13.)

  • Force fields: Amber has two new fixed-charge protein force fields, ff14SB and ff14ipq, a new modular lipid force field, Lipid14, and updates to nucleic acid and carbohydrate force fields.
  • Improved options for self-guided Langevin dynamics and accelerated molecular dynamics, to enchance sampling along soft degrees of freedom.
  • A completely reorganized Reference Manual
  • 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 pmemd for both CPU and GPU platforms, including performance improvements, and support for extra points, multi-dimension replica exchange, a Monte Carlo barostat, ScaledMD, Jarzynski sampling, explicit solvent constant pH, GBSA, and hydrogen mass repartitioning. Support is also included for the latest Kepler, Titan and GTX7xx 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, and a new absolute free energy method.
  • 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.

Amber Tools have also been updated.

Among the new features in AmberTools14:

  • The sander module, our workhorse simulation program, is now a part of AmberTools;
  • Greatly expanded and improved cpptraj program for analyzing trajectories;
  • new documentation and tools for inspecting and modifying Amber parameter files;
  • Improved workflow for setting up and analyzing simulations;
  • new capability for semi-empirical Born-Oppenheimer molecular dynamics;
  • EMIL: a new absolute free energy method using TI;
  • New Free Energy Workflow (FEW) tool automates free energy calculations (LIE, TI, and MM/PBSA-type calculations);
  • Completely reorganized Reference Manual
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GTKDynamo:- Molecular modeling extension for PyMOL

 

GTKDynamo is free/open source software which, together with pDynamo, transforms PyMOL into a powerful interface for molecular modeling. The interface has been designed to facilitate determining reaction pathways in biological systems, specially using hybrid QC/MM (or QM/MM) methods.

Some capabilities include:

  • Pure QC simulations - ab initio and SMO.
  • Pure MM simulations - using AMBER, CHARMM or OPLS force fields.
  • Hybrid QCMM simulations.
  • Single point calculations.
  • Energy minimization.
  • Molecular dynamics.
  • Reaction coordinate scanning.
  • Umbrella sampling.
  • Reaction path calculations - using NEB.

GTKDynamo is available for download for linux and Mac platforms . Please, make sure that you have installed:

  • pDynamo
  • Matplotlib
  • Numpy / Pylab
  • Pymol 1.x
  • pyGTK
  • ORCA, ab initio calculations.

GTKDynamo_overview-page001_800

J. F. R. Bachega, L. F. S. M. Timmers, L. Assirati, L. B. Bachega, M. J. Field, T. Wymore. J. Comput. Chem. 2013, 34, 2190-2196. DOI: http://dx.doi.org/10.1002/jcc.23346

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PYMOL Updated

 

Whilst the update to PYMOL was announced as part of the Schrodinger update I thought it deserved a separate blog entry.

Graphics

  • Greater user control over color settings Color settings can be set as hexadecimal, colors, or floats ( [1., 1., 1.])
  • New ‘focalblur’ command
  • New ‘callouts’ for scene annotations

    Usability

  • Improved and extended Filter Wizard

  • New commands Retrieve bond properties with get_bond Load structures from PubChem by SID and CID codes with fetch
  • Improved PDB Loader graphical interface
  • Expanded documentation of settings
  • Access settings and properties from the iterate/alter commands via “s.” and “p.”
  • Improved labels to include customizable connectors to atoms, multiline labels, and more
  • Ability to select atoms by coordinates or by user-defined property
  • New selection keywords: metals, sidechain, backbone
  • CTRL-F to find objects or selections in the Object Menu Panel

    Bug Fixes

  • Dynamic measures now stored in session files

  • Sequence viewer colors fixed
  • Fixed inversion problem with ‘cealign’
  • Improved stability for shader-based rendering

    AxPyMOL

  • New option to embed content within a PowerPoint file

  • Support PowerPoint PPTX file format
  • Improved installer
  • AxPyMOL control displayed as an “Add In” on the PowerPoint Ribbon
  • 32-bit and 64-bit Office Support
  • Embeddable presentation content
  • Initial support for MAE files
  • Shader-based rendering support for volumes and improved graphics
  • Many bug fixes

The compiled PYMOL binaries are available for paid download with different options for academic, industrial and non-profit.

In addition the source code is available for free download. Not all new features make it to the source code right away, but eventually all features will, usually within a few months

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Schrodinger Small Molecule Drug Discovery Suite Updated

 

The Schrodinger Small Molecule Drug Discovery Suite was updated over the weekend, this is a major update that brings in a host of new features and improvements.

Maestro Graphical Interface

Improved flexible ligand superposition Additional graphics settings
Real-time antialiasing Real-time ambient occlusion, outlines, and cartoon shading effects Multivariate ranking in the Project Table
Simultaneously maximize or minimize up to four property values, and rank entries based on the optimization Date Created and Date Modified fields automatically generated in the Project Table Workspace responsiveness of atom labels is up to 2.5x faster Click and drag to rearrange atom, measurement, and adjustment labels in the Workspace Support for bond labels Installed scripts and Tools menu items now searchable in the Task Tree Significant improvements to the Property Calculation interface in the project facility
Simultaneously calculate multiple properties Additional 2D properties now available: AlogP, #Hbond acceptors, #HBond donors, #rotatable bonds, polar surface area, molar refractivity, and polarizability

Ligand Docking

Ligand efficiencies are now calculated from the DockingScore instead of the GlideScore Generate per-residue interaction energies in Virtual Screening Workflow (VSW) for visualization New server mode in Glide Ligand Designer enables near real-time interactive docking (Glide Ligand Designer Script)

Pharmacophore Modeling

Performance improvements to Phase database operations, including faster deletion and insertion of ligands Automatic restart of Phase database subjobs

Field-Based QSAR

Use QM-calculated fields in 3D QSAR (command line only; phasefqsar script)
phase
fqsar script generates Jaguar input files for computing QM electrostatic fields for use in 3D QSAR

Molecular Dynamics

Monitor secondary structure elements over the course of the trajectory (Simulation Interactions Diagram; SID)

Quantum Mechanics

New interface to compute thermodynamic properties for reactions New faster TDDFT algorithm and graphical interface Compute Raman intensities Several improvements to the results script Jaguar pKa displays the computed pKa as an atom label by default Heat of formation graphical interface now supports bromine and iodine Improved numerical stability of the 1st and 2nd derivatives of the D3 correction Increased utility of canonical.py script
Script acts on a group of isomers and skips structures with unique stoichiometries

Protein X-Ray Refinement

Optionally set hydrogen B-values

Workflows & Pipelining

Includes the latest version of KNIME (v2.9)
Many new features including a Send Email node and ability to save workflows under different names; see http://tech.knime.org/whats-new-in-knime-29 for a complete list of new features Use any Glide simulation option in the Glide Ligand Docking node Employ a specific template in the Prime Build Homology Modeling node Import ungrouped structures to PyMOL from Run PyMOL node

Job Control

Improved fault tolerance Improved handling of suspended jobs in queueing systems

There are also updates to the Biologics Suite and the Materials Science Suite.

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RELEASE OF CLC GENOMICS WORKBENCH 7

 

The new release comes with a long list of new features and improvements such as multi-sample RNA-Seq visualization, a completely new look and feel, and a new beta plugin with a memory-efficient read mapper. A few highlights from the release are:

  • A substantial update of the RNA-Seq Analysis tool
  • New statistical tools for analysis of differential expression
  • A number of new tools now being workflow enabled
  • Several new options for Workflows
  • Great improvements on speed and memory usage for copying data in the Navigation Area and between CLC Genomics Server and a Workbench
  • Complete redesign of the graphical user interface including new options for Side Panels and Views and a redesign of Zoom tools
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Nebiocalculator from New England BioLabs

 

Nebiocalculator from New England BioLabs is actually web app using HTML5, javascript and CSS3, but it has been formatted for touch use so it works nicely on iPhones and iPads. Requires active internet connection.

  • molarity/dilution calculation
  • OD260 conversion
  • ligation calculation
  • mass/moles conversion for both dsDNA and ssRNA

photo

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GenomeBrowse

 

I’ve just been sent a link to GenomeBrowse, this allows the user to explore DNA-seq and RNA-seq pile-up and coverage data in an intuitive manner. Whether viewing one file or many, an integrated approach is taken to exploring your data in the context of rich annotation tracks. Features include: * Zooming and navigation controls that are natural as they mimic panning and scrolling actions you are familiar with. * Coverage and pile-up views with different modes to highlight mismatches and look for strand bias. * Deep, stable stacking algorithms to look at all reads in a pile-up zoom, not just the first 10 or 20. * Context-sensitive information by clicking on any feature. See allele frequencies in control databases, functional predictions of a non-synonymous variants, exon positions of genes, or even details of a single sequenced read. * A dynamic labeling system which gives optimal detail on annotation features without cluttering the view. * The ability to automatically index and compute coverage data on BAM or VCF files in the background.

GenomeBrowse integrates with the powerful Golden Helix SNP & Variation Suite (SVS) analysis platform. SVS can be used to build custom annotations and perform variant analysis, while GenomeBrowse can visualize findings and validate the evidence for putative variants.

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SeqAn

 

I’ve recently been sent details of SeqAn, an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. It is released under BSD/3-clause license and is supported under Mac OS X: GNU/g++, LLVM/Clang (3.0+).

Andreas Döring, David Weese, Tobias Rausch and Knut Reinert. SeqAn an efficient, generic C++ library for sequence analysis. BMC Bioinformatics, 9:11, 2008. DOI

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DNActions widget

DNActions is a Mac OS X Widget that can be used to perform common actions on DNA sequences. It is useful for scientists working in genetics and can be used to obtain the complement reverse of a DNA sequence, the protein translation in all six reading frames (three in the forward strand and three in the reverse), find CpG dinucleotides and calculate the composition and the Tm (melting temperature) of a DNA molecule.