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The missing graphical user interface for genomics

August 24, 2010

Galaxy is an internet based program that provides a trackable, reproducible method for genomic data analysis, and aims to eliminate problems in research that stem from differently analyzed data. The team involved in developing the Galaxy resource believes that an open, web-based approach to genomic analysis will remove the variability stemming from the use of different, unsourced programs.

Read Galaxy Project paper published in Genome Biology»
Visit the Galaxy Project website»

Synthetic biology, creating biological resources from information resources

August 20, 2010

From Riken Research - Databases are becoming increasingly important in the life sciences as a key tool for deriving results. The Bioinformatics And Systems Engineering Division (BASE) is drawing worldwide attention for its SciNeS information infrastructure for handling the vast amounts of data generated through routine research in the life sciences. “A database is not merely a container for data, it is also a place where even life can evolve,” says Tetsuro Toyoda, the director of the BASE. “We can create useful biological resources from information resources by selecting useful genes from databases, designing new genomes, and returning them to the world of living organisms. What databases are needed to realize rational organism design? That is the question we attempt to answer.” To inspire creative use of databases for genome design, the BASE is holding its first International Rational Genome Design Contest.

Read the contest announcement at Riken Research Frontlines»

Sharing of Data Leads to Progress on Alzheimer’s

August 12, 2010

A collaborative effort betwen the NIH, the FDA, and several non-profit groups has resulted in the mapping of a large collection of Alzheimer's Disease biomarkers, the largest expansion of information on the disease in recent history. The study collected information from 800 different brains at different stages of the disease, ranging from the as-of-yet-unaffected to the severely incapacitated, and has resulted in more than100 new drug studies aiming to slow or stop the progression of the disease entirely.

The project, called the Alzheimer's Disease Neuroimaging Initiative (ADNI), has spurred similar collaboration in the field of Parkinson's research, with a 40 million dollar collaborative research initiative by the Michael J. Fox Institute beginning in the next year. Particiants of the ADNI study attribute the success of their study to the heretofore unseen freedom of information that was the standard for the Alzheimer's study.

Read the full article at the New York Times»

Spanish Team Develops Tool to Help Researchers Stay on Top of the Bioinformatics 'Resourceome'

August 06, 2010

A group of Researchers at the Polytechnic University of Madrid, Spain, have developed a tool to automatically compile bioinformatics resources cited in newly published papers, creating the first automatically curated, searchable bioinformatics database. Although the automatically curated Bioinformatics Resource Inventory (BIRI) only contains 230 resources, it is still in its prototype stage. The algorithm used for automating BIRI can extract resources and their functionality with 94% and 88% accuracy, respectively. Although the total number of resources is smaller than in comparable databases, BIRI is the only one of its kind that is automatically curated.

Read the full article at GenomeWeb Daily News» [Paid Subsciption Required]
Read the paper published in BMC Bioinformatics»

NHGRI Pledges $25.5M for Electronic Medical Records (EMR) Program

July 19, 2010

Over the next four years the National Human Genome Research Institute plans to move into the next phase of its electronic medical records research program. NHGRI plans to give out around $25.5 million in grants to fund investigators involved starting a coordinating center for research support. the Electronic Medical Records and Genomics network (eMERGE) that was founded in 2007 will continue to play an important part in the combining of electronic medical recods with DNA biorepositories for use in large-scale, high-throughput genomics research projects.

Read more at the Vanderbildt University homepage for the eMERGE project.

Gonzo Labs Presents The "Dance your PhD" Contest

July 10, 2010

From the Gonzo Labs website - The dreaded question. “So, what’s your Ph.D. research about?” You take a deep breath and launch into the explanation. People’s eyes begin to glaze over… At times like these, don’t you wish you could just turn to the nearest computer and show people an online video of your Ph.D. thesis interpreted in dance form? Now you can. And while you’re at it, you can win $1000, achieve immortal geek fame on the Internet, and be recognized by Science for your effort.

Read more at the contest website.

INCF Image Competition - share your best neuroinformatics images and win prizes sponsored by Olympus and Frontiers

July 6, 2010

The INCF recently launched its first Image Competition on the subject of neuroinformatics! Sharing your best neuroinformatics images with the world could win you one of the prizes sponsored by Olympus and Fronteirs. The INCF Olympus Prize is sponsored by Olympus and has a ¥200 000 (about $2130 USD) prize, awarded to the best neuroinformatics image. The images will be judged based on the criteria of originality, informational content, visual impact, educational value and relevance to INCF Programs, activities and objectives. The INCF Frontiers Prize, awarded to the image best fitting the theme "Brain and Art". The short list for this prize will be picked by the Specialty Chief Editors of Frontiers in Neuroscience, and the final image will be selected by a panel of 5 top-class artists. The winning image will be featured on the cover of the "Brain and Art" e-book from Frontiers in Neuroscience. Submit your image by August 1! Winners will be announced at Neuroinformatics 2010 at the end of August.

Read more at the INCF website.

1000 Genomes Project Releases Data From Pilot Projects on Path to Providing Database For 2,500 Human Genomes

June 30, 2010

The 1000 Genomes Project was launched in 2008 with the goal of creating the most complete and detailed map of human variation to date and has reached completion on three pilot projects. The first three completed projects focused on creating a catalogue of genetic variants present in 1% or more of European, African, and East Asian populations that were chosen for the studies. Further development of the catalogue over the next two years will allow researchers to apply the genetic information within to the study of the genetic variation of illness. The data available on the 1000 Genome website and through Amazon Web Services (AWS) includes a catalogue of single nucleotide polymorphisms (SNPs), small insertions and deletions (indels), and large changes in chromosme structure and copy number (copy number variations).

Read Article at the Sanger Institute website.

View further information about the 1000 Genomes project.

ISB, Gladstone Institute Launch Collaboration Focused on Huntington's Disease

June 16, 2010

From GenomeWeb Daily News – The Taube-Koret Center for Huntington’s Disease Research, a subdivision of the Gladstone Institute of Neurological Disease (GIND), is working with the Institute for Systems Biology (ISB) to catalogue the genes and drug targets that are related to the onset and progression of Huntington’s disease by studying the sequences of whole genomes. This is the largest comparative whole-genome study to-date, and is a methodology that can hiopefully be applied to the study of more common and more complex neurodegenerative diseases.

Read Article at GenomeWeb [Premium subscription required]

Drugmakers to Share Data to Speed Brain Research

June 11, 2010

From Reuters - A collaboration between major drug-makers will share data from Alzheimer and Parkinson’s disease clinical trials. The partnership is coordinated by the Coalition Against Major Diseases and will catalogue the data collected from more 4,000 patients with neurodegenerative diseases, allowing researchers access to a more varied and complete body of information than what is available from individual clinical trials. The database aims to reduce the amount of time that clinical trials will take from beginning to end by increasing efficiency through information availability.

Read Article at the Reuters website.

To request access to the database, click here.

Fed-funded Research Impact Tracker in the Works

June 9, 2010

GenomeWeb Daily News, by Matt Jones - A partnership between NIH and FDP (Federal Demonstration Partnership) ha been launched, with the goal of revamping the reporting practices for federally funded research programs. The program, called STAR METRICS (Science and Technology for America's Reinvestment: Measuring the Effect of Research on Innovation), seeks to ease reporting practices for researchers and make them more transparent for reviewers, ultimately creating a system which better allows for the review of government funding allocations. FDP seeks to achieve this in three ways: the standardizing of reporting practices, collaboration with principal investigators, and a push to demonstrate the impact of scientific investments on a "wide range of outcomes." NIH and FDP hope to create an easy to understand system that will give a clearer picture of how the 3.2 billion dollar budget of the NIH is allocated each year, along with what tangible benefits that allocation of these funds provides.

Read Article [ Premium subscription required. ]

View further information about the STAR METRICS project.

NIH Seek Licensee or Collaborators for Drug Discovery Software

June 4, 2010

From Bioform -The National Institutes of Health is seeking licensees or collaborative partners to work on a software package developed by the National Institute on Aging for analyzing "extremely large experimental data sets in a simple yet multidimensional manner." The software, called Omnimorph, nables users to find "extremely subtle" correlated differences between experimental datasets in order to identify "far more drug- or disease-specific factors than other analytical methods currently used. It has already been used to discover novel G protein-independent receptor-based pharmacotherapeutics, which also makes it "a simple and unbiased tool to detect novel and unexpected modes of GPCR-based drug actions. Omnimorph was developed by Stuart Maudsley, a senior investigator at NIA.

Read Article [ Premium subscription required. ]

View further information about the Omnimorph sofware.

Ariadne and Quertle Partnership to Improve Search Results

June 2, 2010

Quertle, LLC and Ariadne announced a technology partnership that will enhance search results from Quertle's search engine for biomedical literature. Ariadne, which designs and develops software and knowledge integration solutions for pharmaceutical and life science researchers and is a leader in the field, will provide proprietary technology and technical resources to Quertle, packaging it as an appliance solution for the pharmaceutical and agricultural industry.

Quertle is a biomedical search engine focused on delivering informative results to biomedical researchers using advanced linguistic technologies, along with an in-depth understanding of the biomedical field. It will be the first biomedical search engine to focus on meaningful relationships.

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