Today is the final day of Chicago Informatics Week. Actually nine days in all, Informatics Week began on October 30 and ends today, November 7, 2012. All week I’ve been featuring informatics resources in this blog. Today, however, as a final wrap-up, I’m not featuring a resource, but instead focusing a spotlight on some of the many

underway at the Feinberg School of Medicine.

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This entry was posted on November 7, 2012 at 11:44 AM and has received 597 views. There are currently 0 comments.

Informatics is not always about computation, electronic health records, or molecular manipulation. Sometimes when you are doing research in informatics, all you need is a list of identifiers or accession numbers, or you just need to convert a list of identifiers to another format.  Many people don’t know where to turn for such conversion. Today’s featured informatics tool is one of the best for identifier discovery and conversion when searching for Ensembl, UniProt, or Interpro IDs from the European Bioinformatics Institute (EBI):

BioMart

BioMart is part of the suite of tools and databases at the EBI. Other tools are available on the web for identifier conversion, such as DAVID's Gene ID conversion tool, which I mentioned in last Wednesday’s blog. BioMart allows you to start with Entrez/NCBI identifiers, experimental identifiers (eg. Affymetrix) and convert to EBI/Ensembl identifiers, NCBI identifiers and many more.

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This entry was posted on November 6, 2012 at 10:51 AM and has received 546 views. There are currently 0 comments.

Chicago Informatics Week continues. The AMIA Annual Symposium is now underway, and I hope that many Northwestern informatics researchers are attending the conference.

In previous blog posts, I've written about the rise in sequencing experiments in recent years, due to the decrease in costs of sequencing an individual genome. All this sequencing is producing a mountain of data to be analyzed. Many experimenters pay for analysis software or services from the companies that supply the sequencing technology. Other investigators pay a core facility for analysis of sequence data, such as FSM's Bioinformatics Consulting Core. For researchers who want to try analyzing their own data, there are some available options for massive data analysis. Today I feature one such analysis platform:

Galaxy

Galaxy is a web-based open source platform for data-intensive biological research. It is a the product of a collaboration between departments at Penn State and Emory universities, and the tools are hosted at Penn State. The project was funded by numerous grants including awards from the NSF and the NHGRI.

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This entry was posted on November 5, 2012 at 12:15 PM and has received 475 views. There are currently 0 comments.

Happy Day 4 of Chicago Informatics Week!

Today’s featured informatics resource is actually a set of resources. With the increase in sequencing protocols for clinical and basic science research, these featured resources are ever-more valuable tools for getting information about a genomic region.  Today’s feature:

Genome Browsers

There are three major genome browsers used by researchers, but two of them are most heavily used. They are: the Ensembl Genome Browser, the UCSC Genome Browser, and NCBI’s MapViewer.

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This entry was posted on November 2, 2012 at 12:54 PM and has received 1257 views. There are currently 0 comments.

Thanks to reductions in the cost of sequencing individual genomes, individualized medicine and pharmacogenomics are promising to become future reality, rather than the stuff of science fiction. To assess and treat individual phenotypes of specific cancers or other inherited disease, genetic testing is more important than ever. That’s why today’s featured Informatics Week resource is:

The Genetic Testing Registry

The GTR is set to replace well-respected GeneTests in early 2013 as the primary source for locating genetic tests and testing facilities.

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This entry was posted on November 1, 2012 at 11:52 AM and has received 358 views. There are currently 0 comments.

In yesterday’s blog post I wrote about GeneGo MetaCore, a pathway analysis software package that computes network interactions for a set of genes based on evidence from published literature and from Gene Ontology (GO) annotations. Today, I’m featuring two free web resources that rely primarily on GO annotations.  Today’s featured resources:

DAVID and QuickGO

DAVID is a web service hosted by the National Cancer Institute. QuickGO is a web service offered by the European Bioinformatics Institute. They both allow a user to upload a list of molecule identifiers and find enriched GO annotations for that list, but they each have unique features that make them worth trying out.

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This entry was posted on October 31, 2012 at 12:34 PM and has received 417 views. There are currently 0 comments.

Happy Chicago Informatics Week!

As I promised in yesterday's blog post, I will be featuring a different informatics resource every day during Chicago Informatics Week. Today's featured resource is:

GeneGo MetaCore

MetaCore is a pathway analysis software package from GeneGo, a company owned by Thomson Reuters (producers of Web of Science). MetaCore allows users to upload a gene list or dataset from an array experiment and perform enrichment analysis and other network interaction analyses on the data. MetaCore is the only resource I will be featuring this week that is NOT free and open source. However, the Galter Health Sciences Library currently pays the license for this resource so our users can benefit from its powerful network analysis functionality at no charge. To use the GeneGo MetaCore package, users must first register at the Galter website (details below).

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This entry was posted on October 30, 2012 at 12:43 PM and has received 1181 views. There are currently 0 comments.

• Day 1 - October 30, 2012 - Featured Informatics Resource: GeneGo MetaCore
• Day 2 - October 31, 2012 - Featured Informatics Resources: GO Annotation Services DAVID and QuickGO
• Day 3 - November 1, 2012 - Featured Informatics Resource: The Genetic Testing Registry
• Day 4 - November 2, 2012 - Featured Informatics Resource: Genome Browsers
• Day 7 - November 5, 2012 - Featured Informatics Resource: Galaxy
• Day 8 - November 6, 2012 - Featured Informatics Resource: BioMart
• Day 9 - November 7, 2012 - Featured Informatics Resource: FSM Informatics Projects and Research

Chicago mayor Rahm Emanuel has declared Oct. 30 - Nov. 7 2012 as Chicago Informatics Week.  This announcement is scheduled to coincide with Chicago's hosting of the AMIA Annual Symposium, but will include much more than just the AMIA conference. Informatics Week is co-chaired by Justin Starren, Chief of the Division of Health and Biomedical Informatics at Northwestern University Feinberg School of Medicine, and Northwestern is hosting several related seminars and events. The Galter Library is getting in on the Informatics Week fun by posting special blog entries all week and offering a class on the UCSC Genome Browser.

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This entry was posted on October 29, 2012 at 4:18 PM and has received 466 views. There are currently 0 comments.

This week, the National Science Foundation announced changes to its grant proposal guide (GPG). One of the changes is the acknowledgement of datasets, patents, software, and copyrights as citable products of research, eligible for inclusion in a researcher's biosketch. This is a great step forward in providing attribution to researchers' scientific output that falls outside of the traditional realm of manuscripts published in scholarly journals.

According to the GPG Summary of Changes, NSF biosketches have been revised to:

"rename the “Publications” section to “Products” and amend terminology and instructions accordingly. This change makes clear that products may include, but are not limited to, publications, data sets, software, patents, and copyrights." 

Up to 10 total products may be included in the biosketch. Unacceptable products include unpublished papers and invited lectures.

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This entry was posted on October 9, 2012 at 4:23 PM and has received 429 views. There are currently 0 comments.

There's a new cloud data sharing platform available to researchers of all types. Created by a London PhD student, figshare (lowercase "f" intended) is a resource that allows researchers to share figures, datasets, null data and other research output that doesn't make its way into published manuscripts.

Probably the coolest new resource I learned about at this year's VIVO Conference, figshare provides users 1GB of private storage space, plus unlimited public uploads. figshare contains datasets, figures, posters, media and reports of null results. It contains files from many fields of research, from astronomy, physics and biological sciences to humanities. Files in the public space can be commented upon, tweeted and cited via downloads to Reference Manager, EndNote and Mendeley. figshare also provides counts of views, shares and will soon compile citation data on objects at the site.

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This entry was posted on September 12, 2012 at 12:00 PM and has received 1024 views. There are currently 0 comments.