Tregwiki:General websites

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  • Converters:
  • Bibliography, News
    • BARF: Get RSS-feeds for most biology/bioinfo journals here and put them into your...
    • Google Reader to see everyday where new articles appeared in your subjects of interest, then look up bibtex with
    • Jabref Free Citation Manager for Latex
    • highwire Slower, but can show who's citing whom
    • Google Scholar Well, you know it, searches journals in fulltext
    • Connotea is Nature's bibliography and generic link exchange site. You can register, order your bookmarks and bibliography data, tag them and share lists with all other participants.
    • Citulike is (as far as I know, TODO) almost the same thing. You can search both connotea and Citeulike for your keywords and possibly find similar articles in your domain.
    • MEDIE looks pretty useful, a copy of pubmed with different operators, you specify e.g. certain verbs or sequences of words to search
  • Tools for Pubmed
    • hubmed Faster, better than pubmed, can also export to bibtex and put the bibtex into...
    • Pubfinder (article): Give it a list of articles, it will extract the discriminative words and return similar articles
    • Pubmatrix can compare a list of terms against a list of terms, searches all combinations and displays the results in a kind of "cross-matrix" view
    • Chilibot can do multiple pubmed queries for you and displays nice graphics which word is occuring in which abstract.
    • Gopubmed launches pubmed-searches and sorts the results by Gene ontology.
    • iHOP shows a gene-centric pubmed view. Type in any gene and iHOP will display all sentences that contain this gene together with other genes or MeSH terms.
    • Clustermed of Vivisimo is a search engine like Google. Unlike google, it can display it's results clustered into groups which can make sense for pubmed.
    • XPloreMed scan all abstract of a pubmed search and displays the most recurrent words in them.
  • Useless Pubmed Tools:
    • Pubmed Friend a Java interface for pubmed...well...
    • Pubmed Sliders This is the same as pubmed, the only difference is that you can shift sliders to narrow down on your search results. Well...
  • Blogs:
    • Nodelpoint Bioinformatics Blog, I guess the most famous one, in any case, this was the first one that I discovered
    • Flags and Lollypops Bioinformatics Blog
    • Moses Hohman on Inforbiomatica writes a lot about programming languages and bioinformatics and the best approach to develop software
    • Propeller Twist a lot about RNA, general stuff.
    • [1] Good math, bad math is a funny read, but nor really bioinfo-related
    • NaturesNumbers is a much newer blog, less well-known
    • Andrew Dalke an important developer for biopython, is also blogging from time to time
  • Programming, Statistics
    • R The statistics package. I merely use it for simple plotting.
  • Sequence Tools
    • Bioedit The good old free sequence editor (Windows only). Outdated but still usable, especially for biologists. (Update Oct 05: Seems that the author decided to stop distributing it!!! You can still download it if you use google wisely...)
    • Apollo and its siblings ACT/Artemis are not for everyday work, they are just great graphical interfaces to display annotations in any format (GFF, among others).
    • Galaxy looks very promising. Though far from straightforward, it allows every one without programming skills to run analyses on a genomic scale. I guess "extract of all coding regions and display a graph of their lenghts" is something that should be easy with galaxy... (todo)
  • Phylogenetics
  • Whole Genome Data:
    • GenomeSizes : Does what its name implies
    • Metazome : Data of all coding regions clustered into ortholog groups, with genomic neighbours and phylogenetic relationships
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