Galter Health Sciences Library News - Biosciences

BenchFly for Video Protocols, Reviews and a Chuckle

Tue, 17 Nov 2009 13:11:00 -0600

It seems like video protocols are getting more popular, not to mention easier to create and share. You can find scientific how-to videos on YouTube, JoVE and SciVee. This blog has done a feature on JoVE, but submitting to JoVE is not always easy to do: submission fees are pretty steep, especially if you need them to come to your lab and produce your video for you.

If you have a technique or protocol to share and just want to get it "out there", BenchFly offers a good venue for sharing your videos, plus it includes reviews of lab supplies and a blog that is good for a laugh (or a groan).

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Preview the New NCBI Search Homepage

Tue, 20 Oct 2009 10:48:00 -0600

In coordination with the new PubMed interface, the NCBI has also redesigned the Entrez search page.

It's got a fresher look. You can search for data by using the Resources menu (red arrow) or learn how to perform specific searches using the How To... links (green arrow). The databases, such as EntrezGene, EntrezNucleotide and EntrezProtein, haven't changed their look, but the new homepage makes it easier to find a number of databases or tools in a related category, such as Genes & Expression.
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NCBI Sequence Read Archive (SRA) of Next-Generation Sequencing Data

Tue, 15 Sep 2009 11:01:00 -0600

This article was featured in Library Notes #57 (October 2009).

One of the newer databases available from the National Center for Biotechnology Information (NCBI) is the Sequence Read Archive (SRA) of sequencing data. Massively parallel sequencing technologies (sometimes called next generation sequencing) such as 454 (Roche), Illumina, SOLiD (Applied Biosystems), HeliScope, and Complete Genomics can produce gigabases of sequence data.

Researchers who conduct genome sequencing experiments are often searching for a way to share this data with other scientists. The SRA is one way to do this.
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It's About Time! Systems Biology Graphical Notation Standard Created

Fri, 14 Aug 2009 16:27:00 -0600

This article was featured in Library Notes #56 (September 2009).

Electrical circuit diagrams have long had a standard graphical style and notation scheme, but biological systems and processes have not enjoyed the same consistency. Finally, a standard notation for biological systems has been created. The Systems Biology Graphical Notation (SBGN) has been completed and published in Nature Biotechnology, volume 27.

It describes 3 types of graphical standards: a) the process diagram, b) the entity relationship diagram and c) the activity flow diagram (figure from original manuscript). Diagrams can be in color or black and white, and restrictions are not placed on colors used or relative position of elements depicted.
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New NCBI Structure Help Guides

Fri, 31 Jul 2009 11:35:00 -0600

This article was featured in Library Notes #55 (August 2009).

Keeping true to their excellent record of providing high-quality support documentation on their tools and databases, the NCBI has added some new "how-to" guides and documents to their structure databases: 3D Macromolecular Structure and Conserved Domains Database.

The addition of these support documents and added functionality makes the structure resources at NCBI even more powerful and useful to researchers with interest in structure and conserved domain discovery.
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Firefox Add-ons for Scientists and Bitesize Bio's Molecular Biologist's Toolbar

Mon, 13 Jul 2009 12:12:00 -0600

This article was featured in Library Notes #55 (August 2009).

10 (more) reasons to use Mozilla Firefox as your Internet Browser

Nick Oswald, editor-in-chief of the Bitesize Bio blog and Editorial Manager of the journal Neuroendocrinology posted a blog entry on new Firefox Add-ons for scientists. This is a follow-up to his post in 2007 that featured 10 great Firefox add-ons for scientists. Readers are encouraged to also look at this earlier post and try out some of the add-ons.

The current post features i-cite, a mash-up search of content from PubMed, EBI and Google Scholar; it also features such useful tools as a Mac pdf viewer for Firefox, a timer you can run in your browser (really handy for those incubation and rinse steps in your experiments) and a browser add-on link to labmeeting.com.
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New Databases and Tools from EMBL-EBI and NCBI

Mon, 06 Jul 2009 15:16:00 -0600

This article was featured in Library Notes #55 (August 2009).

BioCatalogue.org

EMBL-EBI and the University of Manchester have collaborated in launching a "major new e-science resource": BioCatalogue.org. This site is a curated listing of web-based services, databases and tools. It is meant to provide a one-stop resource for researchers seeking bioinformatics resources.

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New Gene Expression Atlas from EMBL-EBI

Tue, 16 Jun 2009 13:30:00 -0600

On June 15, researchers at the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) launched 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" (quote from the press release(pdf) from EMBL-EBI).

You can search by gene name, up or down regulation, organism, experimental or disease conditions and return results as a heat map or as a list.

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BioSystems: A New Pathway Exploration Tool from NCBI

Fri, 08 May 2009 13:42:00 -0600

This article was featured in Library Notes #53 (June 2009).

The National Center for Biotechnology Information (NCBI) has recently unveiled a new database for pathway and systems exploration: BioSystems.

The BioSystems database was developed by the NCBI as a "collaborative and complimentary project" to databases such as KEGG and BioCyc. BioSystems serves as a centralized repository for data from these other sources, connects this data with the various other database records in NCBI's Entrez system (such as PubMed, EntrezGene, EntrezNucleotide) and provides the user with the ability to access data from each of these sources. [More]

FunDO: Functional Disease Ontology Server

Wed, 22 Apr 2009 13:39:00 -0600

This article was featured in Library Notes #52 (May 2009).

Do you have a list of genes from a microarray experiment and want to see if the gene set is enriched in certain disease profiles? Try a new online tool from Northwestern University Feinberg School of Medicine's own Biomedical Informatics Core (NUBIC). NUBIC is part of the NUCATS clinical and translational science center at the Feinberg School of Medicine, and they are always busy developing new applications that make it easier to visualize and analyze your research.

It's called FunDO, which stands for "Functional Disease Ontology". It is built on a platform of the Disease Ontology project, also created by NUBIC, in collaboration with the NUgene Project at Northwestern's Center for Genetic Medicine.

FunDO enables you to discover new disease associations from a list of input genes, by returning results in an interactive table and graph.

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Get Those Challenge Grants Submitted!

Fri, 17 Apr 2009 09:53:00 -0600

By now, you have probably read about or heard several mentions of the Recovery Act enacted by Congress and the NIH Challenge Grants that have arisen from it. This act contains lots of funding for medical and science research and applications are due April 27. These grants are not full-fledged RO1s, but they do provide funds for researchers to pursue ideas or obtain equipment for projects that have arisen from existing research. The grants are small: the total budget for all 200 of the Challenge Grants is $200 million and no single grant is worth more than $1 million.
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Ingenuity Pathways Analysis is Here!

Thu, 05 Feb 2009 11:06:00 -0600

This article was featured in Library Notes #50 (March 2009).

In response to researchers' requests, Galter Library is pleased to offer Ingenuity Pathways Analysis (IPA) to our user community.

IPA is an application that allows you to explore and discover biomarkers, molecular processes and networks through an interface that integrates scientific literature and molecular databases such as Entrez Gene and Gene Ontology.

Users can learn about canonical pathways and view known interactions, but the true value of IPA is that it allows you to upload high-throughput datasets for analysis. You won't need statistical programming experience to run analyses on your own microarray data.

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Text Mining with CoPub

Mon, 10 Nov 2008 15:11:00 -0600

This article was featured in Library Notes #49 (February 2009).

Free, online text mining tools are scarce and leave a lot to be desired in their functionality. Searching by gene identifiers can a frustrating and elusive task with many databases. You can use the Entrez Gene database or OMIM and link to PubMed results related to the gene you're investigating, but searching MEDLINE directly for gene identifiers returns results that lack both specificity and sensitivity.

CoPub is a search tool that was created to improve searches for genes and biological processes. It was developed by Raoul Frijters and Jan Polman at Organon (part of the Schering-Plough Corporation) and is now hosted and further developed by SARA with support of NBIC.

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SNP Annotation is a "Snap"

Mon, 08 Sep 2008 15:37:00 -0600

This article was featured in Library Notes #48 (Fall 2008).

A common question asked of bioinformatics consultants in libraries is "What can I use for SNP annotation?" The discouraging answer is that there are very few tools that satisfy most users' demands for features in SNP annotation. There are a few, though, that come close. One of these is Snap.

Snap stands for "SNP Annotation Platform", and is hosted by the Institute for Human Genetics at Aarhus University of Denmark. While there are other online and desktop SNP annotation tools, this one is good because it is updated regularly and draws its information from Ensembl, KEGG, UniProt, UCSC, OMIM and Pfam databases.

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JoVE Becomes First Video Journal to be Indexed in MEDLINE

Mon, 25 Aug 2008 16:43:00 -0600

Last week, the Journal of Visualized Experiments (JoVE) was accepted by the National Library of Medicine's ruling committee for indexing in MEDLINE and PubMed. This makes JoVE the first ever video journal to be accepted by the NLM for indexing in MEDLINE. JoVE announced the news in its blog last week.

Numerous protocol journals exist in print format, such as the titles in the Current Protocols series. However, sometimes a picture (or in this case, a video) can be worth a thousand words in conveying proper laboratory technique. JoVE provides video clips of laboratory experiments, organized on its website by category, such as neurosciences, immunology, plant biology, etc.

JoVE is a peer-reviewed, open access journal that began publication in December of 2006. It has received submissions from researchers at institutions such as UC Irvine, Emory, Stanford, Harvard and MIT. The journal welcomes new submissions and JoVE can even send videographers to submitters' labs.

Effective: April 2, 2009: a subscription is required to view most of JoVE video content beyond the first couple of minutes.