Tag Archives: software

BioTorrents — easier, faster exchange of science-related open-access software and datasets

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The goal of BioTor­rents is to allow eas­ier and faster exchange of science-related open-access soft­ware and datasets.
BioTor­rents allows sci­en­tists to rapidly share their results, datasets, and soft­ware using the pop­u­lar Bit­Tor­rent file shar­ing tech­nol­ogy.   (The BioTor­rents website)

From Alain Borel (Bib­lio­theque Sci­en­tifique, Lau­sanne) on the CHMINF List­serv, 1/18/10,  in response to the intro­duc­tion of the sub­ject by Egon Wil­ligha­gen at Upp­sala Univ.:

 
“The dis­trib­uted nature of Bit­Tor­rents sounds nice (it doesn’t mat­ter that zil­lions of users start down­load­ing stuff, since they rapidly all become data sources them­selves). How­ever, I won­der how the updates will be treated? OAI-PMH feels like a much bet­ter pro­to­col from this point of view. Maybe OAI-PMH could be used as a wrap­per for pub­lish­ing and har­vest­ing Bit­Tor­rent seeds (one seed par arti­cle)?” (A.B.)
 
From the web­site:
“The Open Archives Ini­tia­tive Pro­to­col for Meta­data Har­vest­ing (OAI-PMH) is a low-barrier mech­a­nism for repos­i­tory inter­op­er­abil­ity. Data Providers are repos­i­to­ries that expose struc­tured meta­data via OAI-PMH. Ser­vice Providers then make OAI-PMH ser­vice requests to har­vest that meta­data. OAI-PMH is a set of six verbs or ser­vices that are invoked within HTTP.”
…offer­ing Inter­op­er­abil­ity through Meta­data Exchange

VADLO — a search engine for the Life Sciences

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VADLO search engine, devel­oped by 2 biologists, caters to all branches of bio­med­i­cine and life sci­ences. Searchers may delve within five cat­e­gories: Pro­to­cols, Online Tools, Sem­i­nars, Data­bases and Software.

“Pro­to­cols cat­e­gory will let you search for meth­ods, tech­niques, assays, pro­ce­dures, reagent recipes, plas­mid maps, etc. Online Tools will cater cal­cu­la­tors, servers, pre­dic­tion tools, sequence align­ment and manip­u­la­tion tools, primer design etc. Sem­i­nars are essen­tially pow­er­point files for pre­sen­ta­tions, lec­tures and talks. Data­bases will take you to, well, data­bases, resources, com­pi­la­tions, lists etc. It is here that you can also search for your favorite genes and pro­teins. Soft­ware cat­e­gory is for bioin­for­mat­ics experts who are look­ing for codes, scripts, algo­rithms, exe­cuta­bles, down­load­able pro­grams and collaborations”

Direct to VADLO

Taken from the VADLO site, and repro­duced in the lat­est ResourceShelf Newslet­ter, No. 397.