Tag Archives: PID

Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

  • This is not a bad idea. Boston Sci-Geek Tours. I used to work for the Park Service. Hmmm… RT @YishaiKnobel: Fascinating tour and lecture on genomics at Broad Institute today.  Broad should be turned into a Boston tourist attraction. [Mary]
  • RT @BioCatalogue: The BioCatalogue iPhone/iPad app by @manniet3 is now out! http://bit.ly/p2tUQF Please do let us know what you think. [Mary]
  • Includes KEGG, iPATH 2.o, PathwayProjector, metaSHARK, MEGAN 4,  HUMAnN: RT @phylogenomics: A Survey of Metabolic Reconstruction Tools for Metagenomic Datasets » The Bioinformatics Knowledgeblog http://shar.es/HK0U5 [Mary]
  • A Special Symposium Celebrating the 40th Anniversary of the Protein Data Bank, October 28 – 30, 2011, Cold Spring Harbor, NY – Poster Abstract deadline: August 15 [Jennifer]
  • Oh yes, plz: RT @nutrigenomics: like RT @grapealope: Bioinformatics is not just about building tools. We know our tools; we should use them first. @atulbutte #singularityu [Mary]
  • Giggle. I’ve done this with several species, not just plants… : @pcronald: Botanist holds up the entire salad bar. http://onion.com/pojv2t [Mary]
  • RT @wahwahnyc: On PubMed Central: The PathOlogist: an automated tool for pathway-centric analysis. BMC Bioinformatics. http://1.usa.gov/oDyBpc [Mary]
  • Looking for some geeky fun? The Twenty-First 1st Annual Ig Nobel Prize ceremony will occur Thursday, September 29, 2011 and tickets are on sale now. Note: “The Ig Nobel Prizes honor achievements that first make people laugh, and then make them think.” [Jennifer]
  • RT @genetics_blog: . @PLoS and @mendeley_com Call for Apps: http://bit.ly/oc2NGL and http://bit.ly/nHYqNa [Mary]
  • Just saw this in Nature News about Google and Microsoft: Computing giants launch free science metrics [Jennifer]
  • FameLab, a science and engineering communication competition – I haven’t seen an uninteresting one yet… [Jennifer]

Many Protein Resources Have Recently Announced Updates

PDB structure 3rg9

 

 

 

 

In our ongoing pursuit of up-to-date tutorials, I’ve been tracking changes that are occurring at resources and planning our updates accordingly. Protein resources are especially going to keep me out of trouble this summer, because their developers and curators have been busy! I’ve compiled a short synopsis below, and would appreciate comments on any other resources you know about, or want to brag about! :)

  • I featured the ExPASy list of proteomic tools in a past tip. As of  Tuesday this list is no longer being kept up-to-date, but the ExPASy resource has been expanded beyond being “just” a proteomics resource and is now the new SIB Bioinformatics Resource Portal. According to its developers, the portal:

    “provides access to scientific databases and software tools in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc. … On this portal you find resources from many different SIB groups as well as external institutions.”

    And never fear, there is still an up-to-date list of proteomics tools found here.

  • I mentioned in my tip last week that NCBI’s MMDB has undergone an update & I’ll be updating our tutorial on it soon.
  • NCI/Nature Pathway Interaction Database, or PID, had an update June 14th that includes new and updated pathway information.
  • PROSITE had an update June 21st, which is Release 20.73, and now includes 1618 documentation entries, 1308 patterns, 936 profiles and 925 ProRules.
  • The RCSB PDB resource has announced updates to their Browse Database function, enhanced sequence displays from structure summary pages and the PDB-101 educational resource available from blackboard logos on PDB pages. For more details on using PDB, please see our free PDB Introductory tutorial sponsored by the RCSB.
  • STRING’s 9.0 release is now available, and we’ll be looking into anything we need to update in our tutorial as a result.
  • UniProt released an update June 28th that included a major update on many bacterial and archaeal Type II Toxin-Antitoxin modules, as is described here.

Enjoy all the new information – I know I will! :)