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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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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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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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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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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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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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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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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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. 

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