Life Science Research and Drug Discovery at the Turn of the 21st Century: The Experience of SwissBioGrid
Identifieur interne : 000C07 ( Main/Merge ); précédent : 000C06; suivant : 000C08Life Science Research and Drug Discovery at the Turn of the 21st Century: The Experience of SwissBioGrid
Auteurs : Matthijs Den Besten ; Arthur J. Thomas [Royaume-Uni] ; Ralph Schroeder [Royaume-Uni]Source :
- Journal of Biomedical Discovery and Collaboration [ 1747-5333 ] ; 2009.
Abstract
It is often said that the life sciences are transforming into an information science. As laboratory experiments are starting to yield ever increasing amounts of data and the capacity to deal with those data is catching up, an increasing share of scientific activity is seen to be taking place outside the laboratories, sifting through the data and modelling “in-silico” the processes observed “in-vitro.” The transformation of the life sciences and similar developments in other disciplines have inspired a variety of initiatives around the world to create technical infrastructure to support the new scientific practices that are emerging. The e-Science programme in the United Kingdom and the NSF Office for Cyberinfrastructure are examples of these. In Switzerland there have been no such national initiatives. Yet, this has not prevented scientists from exploring the development of similar types of computing infrastructures. In 2004, a group of researchers in Switzerland established a project, SwissBioGrid, to explore whether Grid computing technologies could be successfully deployed within the life sciences. This paper presents their experiences as a case study of how the life sciences are currently operating as an information science and presents the lessons learned about how existing institutional and technical arrangements facilitate or impede this operation.
SwissBioGrid was established to provide computational support to two pilot projects: one for proteomics data analysis, and the other for high-throughput molecular docking (“virtual screening”) to find new drugs for neglected diseases (specifically, for dengue fever). The proteomics project was an example of a large-scale data management problem, applying many different analysis algorithms to Terabyte-sized datasets from mass spectrometry, involving comparisons with many different reference databases; the virtual screening project was more a purely computational problem, modelling the interactions of millions of small molecules with a limited number of dengue virus protein targets. Both present interesting lessons about how scientific practices are changing when they tackle the problems of large-scale data analysis and data management by means of creating a novel technical infrastructure.
In the experience of SwissBioGrid, data intensive discovery has a lot to gain from close collaboration with industry and harnessing distributed computing power. Yet the diversity in life science research implies only a limited role for generic infrastructure; and the transience of support means that researchers need to integrate their efforts with others if they want to sustain the benefits of their success, which are otherwise lost.
Url:
PubMed: 19521952
PubMed Central: 2850249
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000240
- to stream Pmc, to step Curation: 000240
- to stream Pmc, to step Checkpoint: 000635
- to stream PubMed, to step Corpus: 000068
- to stream PubMed, to step Curation: 000068
- to stream PubMed, to step Checkpoint: 000068
- to stream Ncbi, to step Merge: 000089
- to stream Ncbi, to step Curation: 000089
- to stream Ncbi, to step Checkpoint: 000089
Links to Exploration step
PMC:2850249Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Life Science Research and Drug Discovery at the Turn of the 21st Century: The Experience of SwissBioGrid</title>
<author><name sortKey="Den Besten, Matthijs" sort="Den Besten, Matthijs" uniqKey="Den Besten M" first="Matthijs" last="Den Besten">Matthijs Den Besten</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Thomas, Arthur J" sort="Thomas, Arthur J" uniqKey="Thomas A" first="Arthur J" last="Thomas">Arthur J. Thomas</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Oxford Internet Institute, Oxford University, St Giles, Oxford</addr-line>
<country>United Kingdom</country>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Schroeder, Ralph" sort="Schroeder, Ralph" uniqKey="Schroeder R" first="Ralph" last="Schroeder">Ralph Schroeder</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Oxford Internet Institute, Oxford University, St Giles, Oxford</addr-line>
<country>United Kingdom</country>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">19521952</idno>
<idno type="pmc">2850249</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2850249</idno>
<idno type="RBID">PMC:2850249</idno>
<date when="2009">2009</date>
<idno type="wicri:Area/Pmc/Corpus">000240</idno>
<idno type="wicri:Area/Pmc/Curation">000240</idno>
<idno type="wicri:Area/Pmc/Checkpoint">000635</idno>
<idno type="wicri:source">PubMed</idno>
<idno type="wicri:Area/PubMed/Corpus">000068</idno>
<idno type="wicri:Area/PubMed/Curation">000068</idno>
<idno type="wicri:Area/PubMed/Checkpoint">000068</idno>
<idno type="wicri:Area/Ncbi/Merge">000089</idno>
<idno type="wicri:Area/Ncbi/Curation">000089</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">000089</idno>
<idno type="wicri:Area/Main/Merge">000C07</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Life Science Research and Drug Discovery at the Turn of the 21st Century: The Experience of SwissBioGrid</title>
<author><name sortKey="Den Besten, Matthijs" sort="Den Besten, Matthijs" uniqKey="Den Besten M" first="Matthijs" last="Den Besten">Matthijs Den Besten</name>
<affiliation><nlm:aff>NONE</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Thomas, Arthur J" sort="Thomas, Arthur J" uniqKey="Thomas A" first="Arthur J" last="Thomas">Arthur J. Thomas</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Oxford Internet Institute, Oxford University, St Giles, Oxford</addr-line>
<country>United Kingdom</country>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Schroeder, Ralph" sort="Schroeder, Ralph" uniqKey="Schroeder R" first="Ralph" last="Schroeder">Ralph Schroeder</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Oxford Internet Institute, Oxford University, St Giles, Oxford</addr-line>
<country>United Kingdom</country>
</nlm:aff>
<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
</analytic>
<series><title level="j">Journal of Biomedical Discovery and Collaboration</title>
<idno type="eISSN">1747-5333</idno>
<imprint><date when="2009">2009</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>It is often said that the life sciences are transforming into an information science. As laboratory experiments are starting to yield ever increasing amounts of data and the capacity to deal with those data is catching up, an increasing share of scientific activity is seen to be taking place outside the laboratories, sifting through the data and modelling “in-silico” the processes observed “in-vitro.” The transformation of the life sciences and similar developments in other disciplines have inspired a variety of initiatives around the world to create technical infrastructure to support the new scientific practices that are emerging. The e-Science programme in the United Kingdom and the NSF Office for Cyberinfrastructure are examples of these. In Switzerland there have been no such national initiatives. Yet, this has not prevented scientists from exploring the development of similar types of computing infrastructures. In 2004, a group of researchers in Switzerland established a project, SwissBioGrid, to explore whether Grid computing technologies could be successfully deployed within the life sciences. This paper presents their experiences as a case study of how the life sciences are currently operating as an information science and presents the lessons learned about how existing institutional and technical arrangements facilitate or impede this operation.</p>
</sec>
<sec><title>Results</title>
<p>SwissBioGrid was established to provide computational support to two pilot projects: one for proteomics data analysis, and the other for high-throughput molecular docking (“virtual screening”) to find new drugs for neglected diseases (specifically, for dengue fever). The proteomics project was an example of a large-scale data management problem, applying many different analysis algorithms to Terabyte-sized datasets from mass spectrometry, involving comparisons with many different reference databases; the virtual screening project was more a purely computational problem, modelling the interactions of millions of small molecules with a limited number of dengue virus protein targets. Both present interesting lessons about how scientific practices are changing when they tackle the problems of large-scale data analysis and data management by means of creating a novel technical infrastructure.</p>
</sec>
<sec><title>Conclusions</title>
<p>In the experience of SwissBioGrid, data intensive discovery has a lot to gain from close collaboration with industry and harnessing distributed computing power. Yet the diversity in life science research implies only a limited role for generic infrastructure; and the transience of support means that researchers need to integrate their efforts with others if they want to sustain the benefits of their success, which are otherwise lost.</p>
</sec>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Anderson, C" uniqKey="Anderson C">C Anderson</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hey, T" uniqKey="Hey T">T Hey</name>
</author>
<author><name sortKey="Berman, F" uniqKey="Berman F">F Berman</name>
</author>
<author><name sortKey="Hey, A" uniqKey="Hey A">A Hey</name>
</author>
<author><name sortKey="Fox, G" uniqKey="Fox G">G Fox</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Whitley, R" uniqKey="Whitley R">R Whitley</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Shrum, W" uniqKey="Shrum W">W Shrum</name>
</author>
<author><name sortKey="Genuth, J" uniqKey="Genuth J">J Genuth</name>
</author>
<author><name sortKey="Chompalov, I" uniqKey="Chompalov I">I Chompalov</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wooley, Jc" uniqKey="Wooley J">JC Wooley</name>
</author>
<author><name sortKey="Lin, Hs" uniqKey="Lin H">HS Lin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Knorr Cetina, K" uniqKey="Knorr Cetina K">K Knorr-Cetina</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lenoir, T" uniqKey="Lenoir T">T Lenoir</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Star, Sl" uniqKey="Star S">SL Star</name>
</author>
<author><name sortKey="Ruhleder, K" uniqKey="Ruhleder K">K Ruhleder</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gardner, D" uniqKey="Gardner D">D Gardner</name>
</author>
<author><name sortKey="Toga, Aw" uniqKey="Toga A">AW Toga</name>
</author>
<author><name sortKey="Ascoli, Ga" uniqKey="Ascoli G">GA Ascoli</name>
</author>
<author><name sortKey="Beatty, J" uniqKey="Beatty J">J Beatty</name>
</author>
<author><name sortKey="Brinkley, Jf" uniqKey="Brinkley J">JF Brinkley</name>
</author>
<author><name sortKey="Dale, Am" uniqKey="Dale A">AM Dale</name>
</author>
<author><name sortKey="Fox, Pt" uniqKey="Fox P">PT Fox</name>
</author>
<author><name sortKey="Gardner, Ep" uniqKey="Gardner E">EP Gardner</name>
</author>
<author><name sortKey="George, Js" uniqKey="George J">JS George</name>
</author>
<author><name sortKey="Goddard, N" uniqKey="Goddard N">N Goddard</name>
</author>
<author><name sortKey="Harris, Km" uniqKey="Harris K">KM Harris</name>
</author>
<author><name sortKey="Herskovits, Eh" uniqKey="Herskovits E">EH Herskovits</name>
</author>
<author><name sortKey="Hines, M" uniqKey="Hines M">M Hines</name>
</author>
<author><name sortKey="Jacobs, Ga" uniqKey="Jacobs G">GA Jacobs</name>
</author>
<author><name sortKey="Jacobs, Re" uniqKey="Jacobs R">RE Jacobs</name>
</author>
<author><name sortKey="Jones, Eg" uniqKey="Jones E">EG Jones</name>
</author>
<author><name sortKey="Kennedy, Dn" uniqKey="Kennedy D">DN Kennedy</name>
</author>
<author><name sortKey="Kimberg, Dy" uniqKey="Kimberg D">DY Kimberg</name>
</author>
<author><name sortKey="Mazziotta, Jc" uniqKey="Mazziotta J">JC Mazziotta</name>
</author>
<author><name sortKey="Miller, P" uniqKey="Miller P">P Miller</name>
</author>
<author><name sortKey="Mori, S" uniqKey="Mori S">S Mori</name>
</author>
<author><name sortKey="Mountain, Dc" uniqKey="Mountain D">DC Mountain</name>
</author>
<author><name sortKey="Reiss, Al" uniqKey="Reiss A">AL Reiss</name>
</author>
<author><name sortKey="Rosen, Gd" uniqKey="Rosen G">GD Rosen</name>
</author>
<author><name sortKey="Rottenberg, Da" uniqKey="Rottenberg D">DA Rottenberg</name>
</author>
<author><name sortKey="Shepherd, Gm" uniqKey="Shepherd G">GM Shepherd</name>
</author>
<author><name sortKey="Smalheiser, Nr" uniqKey="Smalheiser N">NR Smalheiser</name>
</author>
<author><name sortKey="Smith, Kp" uniqKey="Smith K">KP Smith</name>
</author>
<author><name sortKey="Strachan, T" uniqKey="Strachan T">T Strachan</name>
</author>
<author><name sortKey="Essen, Dcv" uniqKey="Essen D">DCV Essen</name>
</author>
<author><name sortKey="Williams, Rw" uniqKey="Williams R">RW Williams</name>
</author>
<author><name sortKey="Wong, Stc" uniqKey="Wong S">STC Wong</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Podvinec, M" uniqKey="Podvinec M">M Podvinec</name>
</author>
<author><name sortKey="Maffioletti, S" uniqKey="Maffioletti S">S Maffioletti</name>
</author>
<author><name sortKey="Kunszt, P" uniqKey="Kunszt P">P Kunszt</name>
</author>
<author><name sortKey="Arnold, K" uniqKey="Arnold K">K Arnold</name>
</author>
<author><name sortKey="Cerutti, L" uniqKey="Cerutti L">L Cerutti</name>
</author>
<author><name sortKey="Nyffeler, B" uniqKey="Nyffeler B">B Nyffeler</name>
</author>
<author><name sortKey="Schlapbach, R" uniqKey="Schlapbach R">R Schlapbach</name>
</author>
<author><name sortKey="Turker, C" uniqKey="Turker C">C Türker</name>
</author>
<author><name sortKey="Stockinger, H" uniqKey="Stockinger H">H Stockinger</name>
</author>
<author><name sortKey="Thomas, Aj" uniqKey="Thomas A">AJ Thomas</name>
</author>
<author><name sortKey="Peitsch, Mc" uniqKey="Peitsch M">MC Peitsch</name>
</author>
<author><name sortKey="Schwede, T" uniqKey="Schwede T">T Schwede</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hara, N" uniqKey="Hara N">N Hara</name>
</author>
<author><name sortKey="Solomon, P" uniqKey="Solomon P">P Solomon</name>
</author>
<author><name sortKey="Kim, Sl" uniqKey="Kim S">SL Kim</name>
</author>
<author><name sortKey="Sonnenwald, Dh" uniqKey="Sonnenwald D">DH Sonnenwald</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Schroeder, R" uniqKey="Schroeder R">R Schroeder</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Vallas, Sp" uniqKey="Vallas S">SP Vallas</name>
</author>
<author><name sortKey="Kleinman, Dl" uniqKey="Kleinman D">DL Kleinman</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hackett, Ej" uniqKey="Hackett E">EJ Hackett</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Stokes, De" uniqKey="Stokes D">DE Stokes</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hope, J" uniqKey="Hope J">J Hope</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Fore, Joe" uniqKey="Fore J">Joe Fore</name>
</author>
<author><name sortKey="Wiechers, Ilse R" uniqKey="Wiechers I">Ilse R Wiechers</name>
</author>
<author><name sortKey="Cook Deegan, Robert" uniqKey="Cook Deegan R">Robert Cook-Deegan</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lenoir, T" uniqKey="Lenoir T">T Lenoir</name>
</author>
<author><name sortKey="Giannella, E" uniqKey="Giannella E">E Giannella</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Mons, B" uniqKey="Mons B">B Mons</name>
</author>
<author><name sortKey="Et, Al" uniqKey="Et A">al. et</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bairoch, A" uniqKey="Bairoch A">A Bairoch</name>
</author>
</analytic>
</biblStruct>
</listBibl>
</div1>
</back>
</TEI>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Ticri/CIDE/explor/CyberinfraV1/Data/Main/Merge
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000C07 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Merge/biblio.hfd -nk 000C07 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Ticri/CIDE |area= CyberinfraV1 |flux= Main |étape= Merge |type= RBID |clé= PMC:2850249 |texte= Life Science Research and Drug Discovery at the Turn of the 21st Century: The Experience of SwissBioGrid }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Merge/RBID.i -Sk "pubmed:19521952" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Merge/biblio.hfd \ | NlmPubMed2Wicri -a CyberinfraV1
![]() | This area was generated with Dilib version V0.6.25. | ![]() |