Tregwiki:General websites


 * Converters:
 * gene id converter
 * 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.
 * 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
 * The NCBI Taxonomy Browser is handy when dealing with biologists as you can quickly decrypt the names of all those weird species AND you filter on all those animals which are already sequenced (!!). More data on all genomes can be found in the Gold Database.
 * Daniel Pollard made a nice tree of the evoluationary distance of all sequenced flies
 * The Gene Set Builder let's you create lists of genes, share with other people and then transfer them automatically to IDs of other species. Very handy if you want to download the same set of promoters from another species.


 * Workbench-like tools: (list from Jeff Bizarro)
 * Taverna
 * Swami
 * OpenFlow
 * GalaxiaWorkflow
 * Wildfire
 * BIRCH
 * EMBOSS
 * wEMBOSS Portal
 * WSBAW
 * SciCraft
 * Scitegic
 * Pegasys
 * ANGIS
 * W2H


 * 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


 * Tutorials:
 * HMMs
 * Pharyngula: Upstream factor turnover (see discussion papers!) and the bicoid gradient