EMBL-EBI and University of Manchester launch major new e- science resource
Biocatalogue.org – a curated registry of web services for the life sciences – is launched today. Biocatalogue will make it easier for scientists to find bioinformatics services that meet their research needs by providing a single search point. Providers, expert curators and users monitor the catalogue and provide high quality information on each service, including ratings. This type of systematic access has the potential to significantly accelerate the work of biomedical researchers The project has been led by Prof Carole Goble at The University of Manchester and Rodrigo Lopez at EMBL-EBI.

Read more…

• press release from The University of Manchester
• BioCatalogue wiki

On Thursday, July 16, immediately following Genetics Day on the Hill, Genetic Alliance will host Gene Screen: A Night of Film on Health and Genetics. This mini-film festival was open for submissions, and after a competitive selection process, the following films will be screened:

• 6:30 PM Our Dream Come True?
• 6:45 PM Genome: The Future is Now
• 7:05 PM Genetics 101
• 7:10 PM Using Family History to Improve your Health
• 7:20 PM Including Samuel
• 8:20 PM Q&A session with filmmakers

From the basics of biology taught by cartoon characters to the latest advancements in science at Harvard to poignant personal accounts of people struggling with medical conditions, these films are entertaining, emotional, and informative for everyone.

The GeneScreen website also has links to informative webpages fromthe submitters.  Especially nice is the University of Utah’s “Learn.Genetics” site and “Genetics 101” from 23andMe. Please try to attend or support this event if you can!

July 6th: Knowledge mining GeneGo content, EZ Search and MetaSearch

Tired of spending hours searching the public domain building your research objectives? GeneGo now provides a new Google-like interface to search your favorite gene, protein, disease or compound with just one click. In this training session you will learn how to search your favorite gene(s)/protein(s) and obtain a detailed list of references, associated diseases and drugs. We will also demonstrate how to use your search results to further build your hypothesis using network building and gene list exporting functions. GeneGo’s EZ searchable database also includes over 700 prebuilt canonical pathway maps and 842 pre built knowledge networks to facilitate browsing how your proteins interact in key signaling pathways. This session will also take search capabilities to another level where you will learn how to create specific search queries using MetaSearch to generate gene lists for further analysis. Learn how to resolve the following questions:

• What are the diseases associated with my gene?
• I don’t have a gene list, can I still use MetaCore?
• I know my favorite gene is involved in a particular process, but what is the established signaling?
• I have a particular gene list and I want to determine if it is representative of a particular pathway or process approach
• How do I obtain in list of genes to fit my specific queries: ie: What are the enzymes associated with a particular disease?
• What are drugs available to activate or inhibit my protein?
• What genes and diseases are targeted with drug ?
• I have a new compound, are there any similar drugs already available?

Time: Noon (CDT) Central Daylight Time,

Meeting Number: 793 061 365
Meeting Password: Basics123

To join the online meeting:

1. 1. Go to https://genego.webex.com/genego/j.php?ED=110164092&UID=0&PW=b78bde165b6145000d081f5b1610
   2. Enter your name and email address.
   3. Enter the meeting password: Basics123
   4. Click “Join Now”.

July 20th: Identify tissue specific pathology and therapies using novel interactions using MetaLink

Often diseases of an organ, such as the neurological disease, Parkinson’s are caused by manifestation in several tissue regions. Here we demonstrate how novel interactions from different tissues can be used to assign different molecular symptoms to different regions of the brain. We specifically expand on the work of Suzuki et al who obtained expression data on novel Parkin (a gene associated with early onset of Parkinson’s) interaction partners from different regions of the brain known to be affected in Parkinson’s. To introduce custom/novel interactions between Parkin and its binding partners from Suzuki et al, we demonstrate how to generate a MetaLink™ file which allows for automatic visual representation of the custom interactions on networks with known interactions from the database. We then demonstrate how enrichment analysis using MetaCore allows for the specific identification of where each Parkin interacting partner canonical maps. Here we also exploit the visualization properties of GeneGo canonical pathway maps to animate between pathways affected by the loss or gain of Parkin expression and identify tissue specific trends of functionality.

Time: Noon (CDT) Central Daylight Time,

Meeting Number: 798 394 088
Meeting Password: Discovery123

To join the online meeting:

1. 1. Go to https://genego.webex.com/genego/j.php?ED=110103102&UID=0&PW=88f4310c1f125412380316465768
   2. Enter your name and email address.
   3. Enter the meeting password: Discovery123
   4. Click “Join Now”.

On September1, 2009, CRISP (Computer Retrieval of Information on Scientific Projects) will be discontinued and replaced with the Research Portfolio Online Reporting Tool Expenditures and Results (RePORTER) tool:

The NIH has released to the public a beta version of its new Research Portfolio Online Reporting Tool Expenditures and Results (RePORTER) tool.  This new tool retains all of the features of CRISP while providing additional query fields, hit lists that can be sorted and downloaded to Excel, NIH funding for each project (expenditures), and the publications and patents that have acknowledged support from each project (results).  RePORTER also provides links to PubMed Central, PubMed, and the US Patent & Trademark Office Patent Full Text and Image Database for more information on research results.  New features will be added to RePORTER in several releases throughout fiscal year 2010.

Try it out

Take a look at some of the other resources on the Research Portfolio Online Reporting Tool (RePORT) site:

• RePORT Overview
• RePORT Tutorial
• Searchable Public Databases
• Investigators and Trainees
• NIH Data Book
  
• Success Rate
• Crisp/RePORTER
• Reports
• Overview
• Budget and Spending
• …and be sure to browse through the Frequently Requested Reports!

Read more:

Affymetrix is your partner of choice in translating your discoveries into clinical research and making an impact on human healthcare. With a wide range of products and applications, demonstrated commitment to your success, and network of expertise, Affymetrix enables clinical and medical researchers to confidently discover and validate genomic biomarkers.

This summer [Affymetrix] will host a series of conferences featuring high-profile, published scientists who have used Affymetrix technology to advance their medical genomics research. Each conference will last a full day; lunch and snacks will be provided.

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The first three conferences will present pharmacogenomic research approaches to medical genomics, with a particular emphasis on focused panels for investigating drug metabolism markers and chromosome abnormalities. We will also discuss the development of genomic databases for national and international cohorts.

July 13, 2009

Johns Hopkins University
Baltimore, MD

View agenda & register

July 15, 2009

Washington University
St. Louis, MO

View agenda & register

July 17, 2009

City of Hope
Los Angeles, CA

View agenda & register

The second set of conferences will focus on genomic biomarker signature discovery and validation, utilizing applications such as gene expression profiling, miRNA expression, alternative splicing, copy number variation, and loss of heterozygosity. These events are ideal for clinical and medical researchers looking for genetic and genomic signatures associated with disease research.

July 20, 2009

Harvard University
Boston, MA

View agenda & register

July 22, 2009

University of Pennsylvania
Philadelphia, PA

View agenda & register

July 24, 2009

University of Colorado
Denver, CO

View agenda & register

The PLoS Pathogens editors and staff are thrilled to announce the debut of “Pearls,” a new series in the journal that will begin publishing monthly, starting with this June’s issue.

Each Pearl will be a concise primer on a topic of importance, meant to fill the gap between research articles and textbooks. Pearls will be tailored for graduate students and post-docs, while providing a format accessible to a general readership.

In contrast to the dynamic nature of research articles and textbooks, we hope that Pearls will provide a growing compendium of the “lessons that last,” for everyone from the scientist researching an area outside his or her field, to lay readers looking to learn more about a disease that affects them personally.

The benefit of such widely-accessible (not to mention open access!) introductory articles is clear, as evidenced by the level of enthusiasm we found when soliciting potential authors to write the first batch of Pearls. Under the editorial guidance of Dr. Hiten Madhani (University of California, San Francisco) we have seen Pearls grow from a kernel of an idea into what will soon bring focused educational content to readers of the journal.

More than anything, we’re excited to see all the ways in which Pearls may be used once they’re in the public domain: as lab references, class handouts, lecture slides, and undoubtedly in other ways that haven’t even occurred to us yet. We hope you will keep us informed as you find new ways to use them.

Watch for the first Pearl, by Dr. Michael S. Diamond (Washington University School of Medicine), published Friday, June 26 concurrent with an introductory editorial by Dr. Hiten Madhani.

Congrats to Dr. Diamond of WUSM for this inaugural article in the series.

This feature is just one more reason to love the Public Library of Science!!

This month’s issue of Nature Structural & Molecular Biology offers a focus on protein folding with articles such as:

• Editorial: Folding to Function (pp573)
• Converging concepts of protein folding in vitro and in vivo (pp574 – 581) by F Ulrich Hartl & Manajit Hayer-Hartl
• An expanding arsenal of experimental methods yields an explosion of insights into protein folding mechanisms (pp582 – 588) by Alice I Bartlett & Sheena E Radford
• The ribosome as a platform for co-translational processing, folding and targeting of newly synthesized proteins (pp589 – 597) by Günter Kramer, Daniel Boehringer, Nenad Ban & Bernd Bukau
• Unraveling infectious structures, strain variants and species barriers for the yeast prion [PSI⁺] (pp598 – 605) by Peter M Tessier & Susan Lindquist
• Cellular mechanisms of membrane protein folding  (pp606 – 612)  byWilliam R Skach

…and speaking of protein folding, here are a couple of web-based resources for you to check out:

• FOLD-RATE predicts the folding rate of two and three-state proteins with/without structural class information. Read more here: FOLD-RATE — prediction of protein folding rates from amino acid sequence
• FoldX is a a computer algorithm which provides a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes. Read more here: The FoldX web server: an online force field
• The Protein Folding Database (PFD) is a searchable collection of all biophysical data relating to experimental protein folding studies.  Read more here: PFD: a database for the investigation of protein folding kinetics and stability
• KineticDB is a curated database of protein folding kinetics which contains currently experiments on 87 unique proteins and hundred of mutants. The main goal of KineticDB is to provide users with the diverse set of protein folding rates known from experiment. Read more here: KineticDB: a database of protein folding kinetics
• The REFOLD Database – A large number of recombinant proteins expressed in bacteria are insoluble and thus require renaturation. Identifying optimal conditions and methodology for refolding can be time consuming and often rate-limiting. To this end, REFOLD was designed to assist in the design and implementation of methodologies for the in vitro refolding of proteins. Read more here: The Matrix Refolded, REFOLD: An analytical database of protein refolding methods, and The REFOLD database: a tool for the optimization of protein expression and refolding.

To find more databases:

• OBRC: Online Bioinformatics Resources Collection – Health Sciences Library System, University of Pittsburgh
• 2009 NAR Database Summary Papers Category List

Other protein folding resources on the web:

• MIT Open Course Ware: Protein Folding Problem and Protein Folding, Misfolding and Human Disease (check out the readings section)
• Protein folding – Wikipedia
• Folding@home – a distributed computing project — people from throughout the world download and run software to band together to make one of the largest supercomputers in the world. Folding@home uses novel computational methods coupled to distributed computing, to simulate problems millions of times more challenging than previously achieved.
• Rosetta@home - a distributed computing project to determine the 3-dimensional shapes of proteins in research that may ultimately lead to finding cures for some major human diseases.  Read the Quick Guide to Rosetta@home and Its Graphics and Rosetta@home Science FAQ
• Faster Protein Folding Achieved Through Nanosecond Pressure Jump
• HHMI News: Researchers Launch Online Protein Folding Game
• foldit is a computer game enabling you to contribute to important scientific research. Read more…

Stimulated Success

June 19, 2009

As stimulus grants begin to be handed out, the blogger at Medical Writing, Editing & Grantsmanship says you should consider sharing your success story. NIAID has created a page where they will share anecdotes submitted by researchers, asking that investigators “share your successes, both big and small, with us and your community.”

Being able to explore the impact scholarly output has on healthcare practice today is a critical need. It is difficult to get a grasp on the “ripples of impact” that a single discovery can have when we look at only traditional vehicles of conveying information (like conference proceedings and peer-reviewed papers). Incorporating more non-traditional routes of information dissemination may help us gain a greater grasp of the true impact of research and research funding. Very cool idea, indeed.

Mapping gene expression with Gene Expression Atlas
Today, researchers at EMBL-EBI launch a new database, the Gene Expression Atlas, which allows scientists to search and compare gene expression data at unprecedented detail and scope. Observing how gene expression varies in different cell types, tissues and under disease conditions can help researchers understand gene function and to develop new drugs and therapies…more

I can’t wait to take a closer look at this database once I’m back at work – stay tuned!

Conferences, Blogging, and Media

June 04, 2009

Cold Spring Harbor Laboratory is amending its meetings policy so that all participants who plan on blogging and tweeting adhere to the rules sets for members of the media, says a post at Science Insider. Namely, bloggers, media, and tweeters all need to notify CSHL ahead of time if they plan to cover the meeting and must receive permission from the speaker or poster author before reporting on what’s presented. (Full disclosure: This change in policy has been highlighted in part due to a request from GenomeWeb for CSHL to clarify its policy on press rules.) At Daniel MacArthur’s blog, Genetic Future, he and his readers discuss whether meetings should be open or closed — MacArthur blogged from CSHL’s recent Biology of Genomes meeting, which is traditionally “off the record.” He calls CHSL’s policy an “awkward compromise” between the goals of free reporting and discussion of unpublished work. (GenomeWeb’s Editorial Director Bernadette Toner also weighed in at MacArthur’s comment thread.) The question has spread and 2020Science’s Andrew Maynard gives a rundown of when he thinks it’s OK to blog or tweet a meeting. “I think it’s fair to say that there are probably boundaries to appropriate live-tweeting and blogging that still need to be hashed out,” he writes. There is also a discussion on FriendFeed and on MacArthur’s Twitter account.

Interesting point of discussion, indeed! I’ve posted updates of cool things from presentations at conferences – what about you?