Bio Saga Blog - A Chronicle of Life Sciences & Informatics

wwwtilda Data manager in computational material science Introduction Tilde (wwwtilda, ~) is a data manager in cheminformatics and computational material science. The nowadays situation in these disciplines with a plenty of incompatible data formats is rather confusing. Furthermore a new approach to the scientific data verification and exchange is desired because the traditional peer-reviewed journals and their supplementary materials sections do not solve this task properly. Therefore Tilde aims to simplify data processing and exchanging for the scientists, dealing with popular computer simulation packages in material science (e.g.  VASP ,  CRYSTAL ,  WIEN2K  etc). Now the text outputs of these programs can be collected, and the calculated results therein can be visualized. The example focus is on phonon properties of the crystalline materials: vibrational spectra, band structures, densities of states, vibrational patterns visualization etc. Moreover Ti...

A Workshop on Computational Approaches in Biological Data mining is being organised by the Unit Of Simulation and Informatics, Indian Agricultural Research Institute, New Delhi. The topics to be discussed are:- Introduction to Biological databases  Biological data mining  Concept and application of machine learning techniques in bioinformatics  Tools and techniques for bio-molecular prediction  Future directions in biological data mining.  Dates:- March 23rd-25th, 2011. Application deadline:- February 25th, 2011. Do you wish to know more?

Courtesy: B ioclues Job Reference: G586-10LL Genome Discovery Unit, The John Curtin School of Medical Research, ANU College of Medicine, Biology and Environment We are seeking a Genome Computational Specialist to support the work of researchers engaged in cutting-edge projects involving analysis of high throughput sequencing data. Location Canberra/ACT Term of Contract Permanent Grade ANU Senior Manager 1 (Information Technology) Salary Package $88,417 - $92,781 pa plus 17% superannuation Closing Date 3 January 2011 Position Overview The ANU's genomic strategies and expertise has positioned it as a key partner in a number of national and international genomics / phenomics research consortia. The ANU is underpinning this excellence in genomic biology by establishing a Genome Discovery Unit (GDU) for the analysis of high throughput sequencing data. The facility will be staffed by highly skilled personnel who will provide the core expertise for constructing and operating a h...

Canadian-based GPU maker Tycrid Platform Technologies has just announced the launch of the Prometheus Alliance , a collaborative effort aimed at developing cutting edge HPC applications for bioinformatics, with a specific emphasis on next-gen sequencing data and personalized genomics. Chris Heier, President of Tycrid Platform Technologies, stated in a release that "Alliance is being established to address a specific challenge that continues to impede the progress of scientific discovery – the lack of scalable, purpose-built appliances. I feel this is critical as we can virtually eliminate the need for scientists to become computer scientists. Our goal is to take a fresh, innovative approach to developing HPC solutions that do one thing really well – address specific computational challenges for bioinformatics .” XTractor Premium - A Platform for discovery , knowledge sharing, analysis and modelling of published biomedical facts. The only Knowledgebase which provides "...

The National Institutes of Health has awarded 970 stimulus grants worth more than $625 million — around 14 percent of total NIH stimulus grant funding to date — to projects that fall within the broad family of 'omics disciplines, according to a preliminary analysis of the NIH funding database conducted by GenomeWeb Daily News . As of Sept. 30, the close of the fiscal year, the National Institutes of Health had awarded a total of $5 billion in stimulus funding — nearly half of the $10 billion appropriation that NIH will disburse over two years under the American Recovery and Reinvestment Act of 2009 . The $5 billion figure includes both grants and contracts, however. For grants alone, NIH had awarded approximately $4.4 billion via 12,789 ARRA grants as of Oct. 7, according to the database. The 970 grants awarded to 'omics projects comprise 7.5 percent of the stimulus grants awarded so far, but the total funding awarded to these projects makes up 14 percent of NIH ARRA grant ...

The National Institutes of Health has pledged $45 million in grants to establish two new genomics centers at the University of North Carolina at Chapel Hill and at the Medical College of Wisconsin (MCW), as well as to continue funding existing centers at Johns Hopkins University and at the University of Southern California. The two new Centers of Excellence in Genomic Science at UNC and MCW will pursue genomics studies of mental health and gene regulation , respectively. Under the new grants, MCW will receive around $8 million over three years and UNC will reap around $8.6 million over five years from the National Human Genome Research Institute and the National Institute of Mental Health. Johns Hopkins' genomics center will receive around $16.8 million over five years to continue epigenetics of disease studies and USC will use around $12 million over the same period to conduct computational and informatics-based research of genetic variation and disease . "Our aim is to ...

Integrated Genomics gets $250K from Wisconsin State Wisconsin will provide $250,000 to Integrated Genomics through a combination of a loan and a grant, and the company plans to relocate its laboratory and commercial operations from Chicago to Madison, the state's governor's office said Tuesday. The state will give the microbial genomics and gene expression services and technologies company a loan of $200,000 and a grant of $50,000 from the Technology Venture Fund. It said that Integrated Genomics' move could create up to 18 new jobs. Compugen Gets $500K in Grants from Israel The company plans to use the funding to pay for relocating the laboratory to Madison and to buy equipment. Wisconsin Governor Jim Doyle said in a statement that Integrated Genomics "is exactly the type of company our state should be investing in – companies that are developing innovative solutions in the biotechnology industry." Compugen said today that it will receive grants totaling aroun...

We all understand that even the tiniest changes in the environment can create big opportunities and challenges for plants, animals and humans, but rarely do we consider what's happening on a microscopic level and what those changes could mean for the infinite varieties of life on Earth or how mankind's day-to-day experiences could be affected. But University of Houston researchers Yuriy Fofanov and Lennart Johnsson understand that what we don't see often carries big-picture implications. They've recently garnered international recognition for applying such vision while creating technologies to help monitor the sizes and genomic diversity of microbial communities. "The computational tools will pave the way to less expensive and more reliable tests that can be used across the globe. The sheer number of microbial communities presents great commercial potential," said Johnsson, Cullen distinguished professor of computer science, mathematics, and electrical and c...

A new computer-based method of analyzing cellular activity has correctly predicted the anti-tumour activity of several molecules. Research published today in BioMed Central's open access journal Molecular Cancer describes 'CoMet' – a tool that studies the integrated machinery of the cell and predicts those components that will have an effect on cancer. Jeffrey Skolnick, in collaboration with John McDonald, led a team from the Georgia Institute of Technology who have developed this new strategy. As Skolnick explains, "This opens up the possibility of novel therapeutics for cancer and develops our understanding of why such metabolites work. CoMet provides a deeper understanding of the molecular mechanisms of cancer". Identification of metabolites with anticancer properties by Computational Metabolomics The small molecules that are naturally produced in cells are called metabolites. Enzymes, the biological catalysts that produce and consume these metabolites are cr...

Protein domains are the structural and functional units of proteins. The ability to parse proteins into different domains is important for effective classification, understanding of protein structure, function, and evolution and is hence biologically relevant. Several computational methods are available to identify domains in the sequence. Domain finding algorithms often employ stringent thresholds to recognize sequence domains. Identification of additional domains can be tedious involving intense computation and manual intervention but can lead to better understanding of overall biological function. In this context, the problem of identifying new domains in the unassigned regions of a protein sequence assumes a crucial importance. Accumulation of domain information of sequence homologues can substantially aid prediction of new domains. In this paper, we propose a computationally intensive, multi-step bioinformatics protocol as a web server named as PURE (Prediction of Unassigned REg...

HCL founder and chairman and chief strategy officer of HCL Technologies Shiv Nadar was named for the Padma Bhushan honour . Here is yet an interesting and inspiring story of another Shiva, to those aspiring a career in informatics as well as all aspiring entrepreneurs. In the 26 years since he first arrived at MIT as a freshman, V.A. Shiva Ayyadurai has earned four MIT degrees and started two multimillion dollar companies. This fall, he will use his most recent degree, a Ph.D. in computational systems biology, and a Fulbright Scholarship to explore one of his lifelong interests: the intersection of Eastern and Western medicine. Ayyadurai started dreaming as a child in India, where his grandfather was a farmer and his grandmother a shaman, or traditional healer. He became interested in medicine watching his grandmother diagnose and treat patients based on a system of "elements"--earth, water, fire, metal and wood. That approach may seem strange to Westerners, but "you...

An “ecosystem” of partners who will use programmable hardware to create a standardized approach for analyzing data from second-generation sequencing instruments. Intel Seeks Partners to Develop FPGA-Based Solution for Next-Gen Sequencing Analysis . “Primary data analysis seems to be where Intel can play the most useful role” in the field, considering the initial analytical steps in sequencing: image processing, base calling, and alignment and assembly. One downside to this scenario, however, is that these codes would need to be written for FPGA-based systems – a very specialized programming skill that many bioinformatics developers don’t have. This challenge could present an opportunity for companies that develop FPGA-based algorithms and software-development toolkits. While the task of harvesting data from second-generation sequencing instruments has only just begun, both large and small labs are already facing some big choices over how to store the terabytes of data that these tools...

IMGT®, the international ImMunoGeneTics information system ( http://imgt.cines.fr ), is the reference in immunogenetics and immunoinformatics. IMGT standardizes and manages the complex immunogenetic data that include the immunoglobulins (IG) or antibodies, the T cell receptors (TR), the major histocompatibility complex (MHC) and the related proteins of the immune system (RPI), which belong to the immunoglobulin superfamily (IgSF) and the MHC superfamily (MhcSF). The accuracy and consistency of IMGT data and the coherence between the different IMGT components (databases, tools and Web resources) are based on IMGT-ONTOLOGY, the first ontology for immunogenetics and immunoinformatics. IMGT-ONTOLOGY manages the immunogenetics knowledge through diverse facets relying on seven axioms, ‘IDENTIFICATION’, ‘DESCRIPTION’, ‘CLASSIFICATION’, ‘NUMEROTATION’, ‘LOCALIZATION’, ‘ORIENTATION’ and ‘OBTENTION’, that postulate that objects, processes and relations have to be identified, d...

Have you been wondering about possibility of automating every scientific workflow? : The Taverna Interaction Service: enabling manual interaction in workflows by Anders Lanzén and Tom Oinn Taverna is an application that eases the integration of tools and databases for life science research by the construction of workflows. The Taverna Interaction Service extends the functionality of Taverna by defining human interaction within a workflow and acting as a mediation layer between the automated workflow engine and one or more users. Try Taverna plugin is very likely an answer to automation of bioinformatics workflows... (Bioinformatics Advance Access abstract)