Bioinformatics

Only ten days left to register! - Rutger Vos

"What's Phylo all about? Though it may appear to be just a game, Phylo is actually a framework for harnessing the computing power of mankind to solve a common problem; Multiple Sequence Alignments." - Mickey Kosloff from Bookmarklet

"UTGB (University of Tokyo Genome Browser) Toolkit is an open-source software for developing personalized genome browsers." - Mike Chelen from Bookmarklet

Hosted on Google code: https://code.google.com/p... - Mike Chelen

Hmm, looks outdated. Pity because PHP fits together so well with web servers. - Mike Chelen

Ah, will be talking about "Structure-based redesign of protein-protein interaction specificity reveals mechanism and selectivity of G-protein turn-off by RGS proteins". - Mickey Kosloff

Can you please share the link ? Thanks. - Khader Shameer

This seems to be the right link: http://www.nrbsc.org/anton_r... - Mickey Kosloff

It took many years for mandatory submission of structures to the PDB. Structure factor deposition became mandatory only recently. Maybe this petition will help shorten the time lag for what seems to be the logical next step with cryoEM data? - Mickey Kosloff from Bookmarklet

"One of the biggest issues you face when you first start doing molecular dynamics (MD) simulations is how to create an initial geometry that won’t blow up in the first few time steps. Repulsive forces are very steep if the atoms are too close to each other, and if you are trying to simulate a condensed phase (liquid, solid, or interfacial) system, it can be hard to know how to make a sensible initial structure. Packmol is a cool program that appears to solve this problem. It creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short range repulsive interactions do not disrupt the simulations. The great variety of types of spatial constraints that can be attributed to the molecules, or atoms within the molecules, makes it easy to create ordered systems, such as lamellar, spherical or tubular lipid layers. It works with PDB and XYZ files and appears to be available under the GPL. Very, very cool!" - Mike Chelen from Bookmarklet

"ProteomeCommons is a public repository for digital content relating to proteomics, and a foundation for building a useful online community. We provide public access to free, open-source proteomics-related tools and allow researchers to share data using Tranche." - Mike Chelen

Post-challenge submissions are also possible, in a sense: http://tunedit.org/challen... - Marcin Wojnarski

"Serving as an introduction to computational biology, this course emphasizes the fundamentals of nucleic acid and protein sequence analysis, structural analysis, and the analysis of complex biological systems. The principles and methods used for sequence alignment, motif finding, structural modeling, structure prediction, and network modeling are covered. Students are also exposed to currently emerging research areas in the fields of computational and systems biology." - Mike Chelen from Bookmarklet

"We introduce TreeVector, a Scalable Vector Graphics–and Java-based method that allows trees to be integrated and viewed seamlessly in standard web browsers with no extra software required, and can be modified and linked using standard web technologies. There are now many bioinformatics servers and databases with a range of dynamic processes and updates to cope with the increasing volume of data. TreeVector is designed as a framework to integrate with these processes and produce user-customized phylogenies automatically. We also address the strengths of phylogenetic trees as part of a linked-in browsing process rather than an end graphic for print." - Mike Chelen

Convert Newick Tree Topogies to SVG Trees online or download the source, http://supfam.cs.bris.ac.uk/TreeVec... - 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

"DIYbiology (“DIYbio”) is a homegrown synthesis of software, hardware, and wetware. In the tradition of homebrew computing and in the spirit of the Make space (best typified by o‘Reilly‘s Make Magazine), these DIYers hack much more than software and electronics. These biohackers build their own laboratory equipment, write their own code (computer and genetic) and design their own biological systems. They engineer tissue, purify proteins, extract nucleic acids and alter the genome itself. Whereas typical laboratory experiments can run from tens-of-thousands to millions of dollars, many DIYers knowledge of these fields is so complete that the best among them design and conduct their own experiments at stunningly low costs. With adequate knowledge and ingenuity, DIYbiologists can build equipment and run experiments on a hobbyist‘s budget. As the movement evolves, cooperatives are also springing up where hobbyists are pooling resources and creating “hacker spaces” and clubs to further reduce costs, share knowledge and boost morale." - imabonehead from Bookmarklet

Found it via Slashdot (http://science.slashdot.org/story...) - imabonehead

Definitely! It's a very cool logo. - imabonehead

"The MGED Society is an international organization of biologists, computer scientists, and data analysts that aims to facilitate biological and biomedical discovery through data integration. Our approach is to promote the sharing of large data sets generated by high throughput functional genomics technologies. Historically, MGED began with a focus on microarrays and gene expression data. However, the scope of MGED now includes data generated using any technology when applied to genome-scale studies of gene expression, binding, modification and other related applications. Members of MGED work to establish standards for data quality, management, annotation and exchange; facilitate the creation of tools that leverage these standards; and work with other standards organizations and promoting the sharing of high quality, well annotated data within the life sciences and biomedical communities." - Mike Chelen

Conference URLs : http://cs.nyu.edu/parida... | http://www.webdevelopment4ri.com/ncbs... Details about the local transport and venue : http://apbc2010.blogspot.com/ - Khader Shameer from Bookmarklet

stack overflow is well regarded for the post rating system. there are some informative, and some annoying posts on either site though ;) - Mike Chelen

Mike, I believe that describes most sites. Well, sites with users anyway. - Akiva

Akiva: maybe the question is whether the site design helps users find posts that are informative to them? - Mike Chelen

"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