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.

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

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.

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)

JTreeView renders gene expression data into several interactive views.

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

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 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.