Tip of the Week: Year of Tips, part deux

As Trey posted last week in part I, we’ve been doing tips-of-the-week for two years now. We have completed over 100 little tidbit introductions to various resources*.  At the end of the year 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.

I’ve got the second half of this year to summarize–July through December 2009. Check them out!

July 2009

7/1  UCSC wiki annotations UCSC has created a way for anyone to add annotations to their genes of interest using a wiki.

7/8  CellMiner from NCI A relational database for cancer cell line data.

7/15  ENCODE data at UCSC The Data Coordination Center, or DCC, for the human ENCODE data is introduced, with guidance on how to access ENCODE data in the UCSC Genome Browser.

7/22  It’s a duplicate Check out Deja Vu, a program to assess scientific abstracts for similarity, including duplication or possible plagiarism events.

7/29 VirusMINT The Molecular Interaction Database that we love added a component for Virus protein interactions.

August 2009

8/5  Genomic Encyclopedia of Bacteria & Archaea (GEBA) This piece on the strategy of choosing new genomes to sequence was introduced in August.  If this is of interest to you, also check out the recent publication about this project that we talked about here.

8/12  NCBI’s New BioSystems Resource Wherein NCBI takes on the storage and representation of biological network data.

8/19  PLAN2L for Arabidopsis literature A helpful tool for literature searching for Arabidopsis.

8/26  Acytelome, String and a new database An introduction to the Phosida database, for phosphorylation and acetylation information.

September 2009

9/2 A mouse for all reasons Learn about the knockoutmouse.org site, which provides information and reagents for generating knockout mice.

9/9  TARGeT A resource for identifying transposable elements and genes relationships from sequence submissions.

9/16  The National Center for Biomedical Ontology This central repository for Ontologies can be really helpful for bioinformatics software project developers.

9/23  JBrowse, a game changer? A look at a new strategy in genome browsing software.

9/30  Finding the right genomics resource This is a quick introduction to OpenHelix’s own new interface for searching for training movies and materials!

October 2009

10/7  NCBI Makeover! The overhaul of the NCBI interface–with a walk through memory lane at some of it’s previous incarnations–is provided.

10/14  Getting flanking sequence A quick look at how to use Galaxy to obtain adjacent sequences, which is a question we are asked frequently in training situations.

10/21  SwissVar, a New Genotype-phenotype Resource from SIB Explore ‘a portal to Swiss-Prot diseases and variants.’

10/28  Sol Genomics Network Do you like tomatoes, eggplants, potatoes, peppers, and other members of the Solanaceae? If so, check out this resource.

November 2009

11/4  CHOP CNV database If you are curious about copy-number variations, be sure to explore the collection at CHOP.

11/11  GeVo and Genome Comparison A nifty tool for genomic comparisons.

11/18  FABLE, text mining for literature on human genes A literature mining resource to improve you searching.

11/25  Got tips for us? We opened the floor for suggestions of tools to look at as we celebrated the Thanksgiving holiday.  We’ll still take suggestions–we love to explore new resources!

December 2009

12/2  RCSB PDB Comparison Tool Compare sequences for structural similarities with this handy widget.

12/9  GRAIL for prioritizing SNPs Use a list of SNPs to identify associated genes, and then sweep the literature for leads on the processes that might be involved.

12/16  GenomePad Check out this very cool iPhone app for exploring the UCSC Genome Browser.

12/23  Tip of the Week: Year (2nd!) of Tips for the first half of the year’s summary of tips.

*for the vast majority of resources we introduce in our tips, we have no financial relationship with the provider or developer. The ones we do are listed here.

One thought on “Tip of the Week: Year of Tips, part deux

  1. Pingback: Tip of the Week: A year of tips III (first half of 2010) | The OpenHelix Blog

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