Tag Archives: SIB

Video Tips of the Week: Annual Review IV, 2nd half

As you may know, we’ve been doing these video tips-of-the-week for FOUR years now. We have completed around 200 little tidbit introductions to various resources from last year, 2011 (yep, it’s 2012 now). At the end of the year we’ve established a sort of holiday tradition: we are doing a summary post to collect them all. If you have missed any of them it’s a great way to have a quick look at what might be useful to your work.

You can see past years’ tips here: 2008 I2008 II2009 I2009 II2010 I2010 II. The summary of the first half of 2011 is available from last week.

July 2011

July 6: Prioritizing genes using the Gene Prioritization Portal

July 13: PolySearch, searching many databases at once

July 20: Human Epigenomics Visualization Hub

July 27: The new SIB Bioinformatics Resource Portal

 

August 2011

August 3: SNPexp, correlation between SNPs and gene expression 

August 10: CompaGB for comparing genome browser software

August 17: CoGe, comparing genomes revisited

August 24: Domain Draw for quick motif diagrams

August 31: From UniProt to the PSI SBKB and back again

 

September 2011

September 7: Plant comparative genomics using Plaza

September 14: phiGENOME for bacteriophage genome exploration

September 21: Getting flanking sequences of genomic locations

September 28: Introduction to R statistical software 

 

October 2011

October 5: VnD resource for genetic variation and drug information

October 12: Track Hubs in UCSC Genome Browser

October 19: Mitochondrial Transcriptome GBrowser 

October 26: Variation data from Ensembl

 

November 2011

November 2: MizBee Synteny Browser

November 9: The new database of genomic variants: DGV2

November 16: MapMi, automated mapping of microRNA loci

November 23: BioMart’s new central portal

November 30: Phosphida, a post-translational modification database

December 2011

December 7: VarSifter, for identifying key sequence variations

December 14: Big changes to NCBI’s genome resources

December 21: eggNOG for the Holidays (or to explore orthologous genes)

December 28: Video Tips of the Week: Annual Review IV (first half of 2011)

Tip of the Week: the New SIB Bioinformatics Resource Portal


A few years ago I did a tip on the proteomic tools list available from the ExPASy site. You can still get to that list, but it is no longer being updated. Instead the entire ExPASy site has been updated and reorganized and is now the new Swiss Institute of Bioinformatics (SIB) Bioinformatics Resource Portal. In today’s tip I want to explore the updated site & show you a few of the new features.

ExPASy was created in 1993, and was one of the first resources online for biomedical research. It has been a great resource for years, and you can learn a lot about their history and goals from their original paper (referenced below). But they have also evolved. According to the ExPASy press release:

Eighteen years later, ExPASy is still an indispensable resource worldwide. Its transformation into a bioinformatics resource portal with the possibility to search for data in various interconnected fields such as proteomics, genomics, phylogeny, systems biology, evolution, drug design and imaging will allow
life science researchers to optimise their research activities through access to an enriched set of high-quality data.

The updated site allows researchers to access the SIB content using Visual Guidance, Categories, an alphabetized list or through querying the site. I’ll quickly show you most of these methods. Once you know how to search the ExPASy site, you’ll have a powerful access point for finding and querying over 120 SIB resources. OpenHelix has a huge respect for the resources that the SIB groups have created, and we have created tutorials on many of them including PROSITE, STRING, and UniProt. We also touch on many others in tutorials or tips, so if you’d like more details than are offered in the SIB resource documentation, use our search portal to see what we have on the resource. If there are SIB resources that you’d like to see us develop on, please comment and let us know – we’re always happy to add another useful resource to our international resource list, which currently includes thousands of resources.

Quick link to the SIB Bioinformatics Resource Portal:  http://www.expasy.ch/

Reference:
Gasteiger, E. (2003). ExPASy: the proteomics server for in-depth protein knowledge and analysis Nucleic Acids Research, 31 (13), 3784-3788 DOI: 10.1093/nar/gkg563