Bioinformatics

"I’ve gone back to using another wonderful visualization package, PyMol. I find that it hits the sweet spot between easy setup of the scene I’d like and generating nice figures. The specific feature that I’ve come to rely on quite heavily is the built-in ray tracer. There are three available ray tracing modes in addition to the default, each of which has its uses. Mode 1 will place a black outline around your structure, which can help make the secondary structure elements visually distinct. Mode 2 is really interesting, in that it only renders the outline. I find this especially helpful if I want to show something in an overlay without obscuring what is behind it. Mode 3 produces “quantized” color in addition to the outline, giving your figure a very cartoonish appearance. I find that this one has to be used with care :) " - Mike Chelen from Bookmarklet

"The OBO Foundry is a collaborative experiment involving developers of science-based ontologies who are establishing a set of principles for ontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain. The groups developing ontologies who have expressed an interest in this goal are listed below, followed by other relevant efforts in this domain." - Mike Chelen from Bookmarklet

"The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases. The project provides a controlled vocabulary of terms for describing gene product characteristics and gene product annotation data from GO Consortium members, as well as tools to access and process this data." - Mike Chelen from Bookmarklet

sourceforge project page: https://sourceforge.net/project... - Mike Chelen

"Analytical Services, Databases and Software" - Mike Chelen from Bookmarklet

"This paper presents an FPGA-based accelerated solution for DNA sequencing and dot plotting. It describes how multiple FPGA devices can be deployed to create a scalable cluster dedicated to the task of analyzing large amounts of data, and how this clustered hardware application can be connected to a software application for visualization and analysis." - imabonehead from Bookmarklet

"PhyLIS is a user-friendly, free linux distribution for phylogenetics. Install it and you have an instant phylogenetics workstation. No downloading packages or messing with compilers, no configuring software, no worrying about small differences between systems that mess up your scripts. Simply install, sit down, and work. PhyLIS started during a period when I was acquiring several new computers for a large phyloinformatic project and grew tired of installing general purpose linux distributions, and then having to spend an hour or two reconfiguring everything and adding software on each new computer. I began developing scripts that would do some of this work for me, eventually they became overly-complicated, and I still had to carry around thumbdrives full of software or needlessly re-download everything. Eventually it just became more desirable to have an operating system that was specifically geared towards doing phylogenetics. PhyLIS is based on Ubuntu linux, a widely used... more... - Mike Chelen from Bookmarklet

trying to determine if the information can be pulled any ways besides html? maybe they will move to SMW soon :) - Mike Chelen

"fpocket is a very fast open source protein pocket (cavity) detection algorithm based on Voronoi tessellation. It was developed in the C programming language and is currently only available as command line driven program. A GUI is in development. fpocket includes two other programs (dpocket & tpocket) that allow you to extract pocket descriptors and test own scoring functions respectively. As the algorithm is very fast it can be used on a large scale level (PDB size for instance)." - Mike Chelen from Bookmarklet

the open data table adapts the query URL parameters and specifies the series of elements to return. source code: http://github.com/mchelen... - Mike Chelen

all three tables are available using a custom environment, for example with esearch: http://bit.ly/27tTVn - Mike Chelen

"A dedicated bioinformatics workstation - install it or run it live. Bio-Linux provides more than 500 bioinformatics programs on an Ubuntu Linux base." - Mike Chelen from Bookmarklet

Deepak: that's good, been trying to find a way to get the bio-linux packages installed on 64bit instance. desktop could be handy for learning and testing - Mike Chelen

"This package contains function for reading and displaying PDB-files from the Brookhaven protein databank in Octave, a scientific computation software." - Mike Chelen from Bookmarklet

coming soon to a koala near you! - Mike Chelen

"ZenPDB is a Python module to process and analyze macromolecular structures. Macromolecular structures are represented as hierarchically nested python dictionaries, which allows to traverse and manipulate them in a pythonic way and implement structural biology algorithms compactly. This module is also useful to establish processing pipelines. ZenPDB is currently capable of parsing and writing PDB files, but PDBML input is also planned. ZenPDB provides fast and versatile Cython implementations of important algorithms in structural biology, namely accessible surface area (ASA) and distance contact calculations by using kd-trees for nearest neighbour look-up. It is crystallography-aware and can construct crystal lattices, unit cells and biological units." - Mike Chelen from Bookmarklet

"This package contains some ribosomal RNA BLAST databases distributed as part of the NCBI C Toolkit that are too large and specialized to include in ncbi-data. Specifically, it contains the databases Combined16SrRNA_2-12-2008, LSURef_93.fasta, and SSURef_93.fasta, along with an alias file to facilitate searching all three of them in conjunction with the 16SCore database included in ncbi-data." - Mike Chelen from Bookmarklet

"Nesoni is a high-throughput sequencing data analysis toolset, which the VBC has developed to cope with the flood of Illumina, 454, and SOLiD data now being produced. Our work is largely with bacterial genomes, and the design tradeoffs in nesoni reflect this. Nesoni focusses on analysing the alignment of reads to a reference genome. We use the SHRiMP read aligner, as it is able to detect small insertions and deletions in addition to SNPs." - Mike Chelen from Bookmarklet

"The Rotamerically Induced Perturbation (RIP) method generates local perturbations that are capable of inducing several Ångstroms of conformational change in just picoseconds of a Molecular-Dynamics (MD) simulation. It is particularly useful for identifying potentially mobile loops and helices in a protein structure." - Mike Chelen from Bookmarklet

The RIP code is released under GPL, however it does require the closed-source AMBER program. - Mike Chelen

"The available amount of data in bioinformatics is huge. One way to characterize for example protein function is to perform large-scale analyses on the available data. These analyses are to an increasing extent dependent on fast computers. The demands are similar for most bioinformatics groups within the Nordic countries and it therefore makes sense to coordinate common efforts. Presently, bioinformatics resources are available within each country but with limited coordination between the countries. With a Nordic bioinformatics grid infrastructure heavy computational tasks can be performed faster and more efficiently." - Mike Chelen from Bookmarklet

"Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. URL: http://cytoscape.org/" - Mike Chelen from Bookmarklet

"ViPDAC uses Amazon Web Services to analyze proteomics data." - Mike Chelen from Bookmarklet

"The Distributed Annotation System (DAS) defines a communication protocol used to exchange annotations on genomic or protein sequences. It is motivated by the idea that such annotations should not be provided by single centralized databases, but should instead be spread over multiple sites. Data distribution, performed by DAS servers, is separated from visualization, which is done by DAS clients." - Mike Chelen from Bookmarklet

"Applied Bimatics - A Bioinformatics Blog" - Bell Eapen from Bookmarklet