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Friday, October 14, 2011

So what tools are European Bioinformaticians using? Part 1

We blogged at the end of September about an article in ecancermedicalscience covering a paper which documented usage of caBIG tools and technologies by European researchers - the basic findings of the repot were that the tools are not widely used (these are tools designed to produce "an integrated informatics grid to incorporate open source, open access tools to collect, analyse and share data, enabling everyone to use the same methods and language for these tasks") but that where they are, they are very highly rated.

The feedback we had when we spoke to some friends at caBIG was that this was no big surprise as their efforts had been directed at the US biomedical enterprise and they had not made any serious investment in promoting their offering in Europe...

We thought the headline of the article ("European cancer researchers failing to use research tools") might raise a few eyebrows with other friends of ours at research institutes across the UK who most certainly are using research tools - so we thought we'd set about finding out what tools are available in Europe and who is using what.

First stop, the European Bioinformatics Institute - OK, so they don't focus on cancer, but the tools they offer clearly have an application in various aspects of cancer research - in their own words, the most popular of them "include tools for the analysis and comparison of nucleotide and protein sequences, data from functional genomics experiments, text mining of the scientific literature and tools for determination and visualisation of macromolecular structures. All these tools can be accessed over the web and most provide Web Services interfaces using SOAP orREST APIs."

For more detail, see the EBI tools page - but in summary, they offer tools covering:
  • Nucleotide sequence searches x2 (across various database including EMBL-Bank, Coding Sequences, immunoglobulins and High throughput cDNA)
  • Protein sequence searches x2 (across database including UniProtKB, sequences derived from macro molecular structures, immunoglobulins and sequences from patents)
  • Multiple sequence alignment tools x5!
  • Pairwise sequence alignment tools x2
  • Functional genomics tools x3
  • Potein function analysis tools x4
  • Molecular structural analysis tools x2
  • Scientific literature text mining tools x2
  • And five data retrieving and ID mapping services:
Over the next week we are going to look in more detail at some of the tools being used in the UK from micro-array technologies to clinical data management systems - including those from the EBI listed above - and how these are being linked to derive new insights...  use any yourself which you particularly rate? Then let us know!

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