Postdoc position: Structural Bioinformatics/Big Data at UC San Diego
"Rose, Peter" <[email protected]> Mon, 2 May 2016 21:46:12 +0000
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <D34D18B3.2D2C2%[email protected]> |
--===============7552460431934394101== Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_D34D18B32D2C2pwroseucsdedu_" --_000_D34D18B32D2C2pwroseucsdedu_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Summary: We are looking for a highly motivated postdoc as part of our new p= roject =93Compressive Structural Bioinformatics=94 funded by the US Nationa= l Institutes of Health (NIH) Big Data to Knowledge (BD2K) initiative. The Challenge: To enable efficient research on the rapidly growing number o= f 3D molecular structures of ever increasing size and complexity. Current a= lgorithms used in Structural Bioinformatics do not scale well with the rapi= d growth in structural data. In this project, we will employ the latest adv= ances in computer science to develop highly scalable, distributed parallel = algorithms to overcome these limitations. Qualifications: Ph.D. in one or more of the following research areas =B7 Computer Science with a focus on large scale scientific computing =B7 Structural Bioinformatics with a focus on new methods development =B7 Computational Structural Biology with a focus on improved structur= e solution methods Experience with the development and performance optimization of scientific = software. Demonstrated proficiency in a high-level programming language, su= ch as Java or Python and experience with state of the art software developm= ent tools. Strong skills in applied mathematics and algorithm design are re= quired. High productivity demonstrated by publications and contributions to= open source software projects. Experience in the development and applicati= on of modern distributed parallel computing environments, such as Apache Bi= g Data projects including Apache Spark is a plus. Excellent interpersonal, = written, and oral presentation skills are essential. Note, this position is reviewed annually on the basis of performance and ca= n be renewed for a maximum of two years. Our Environment: The Structural Bioinformatics Group (http://bioinformatics.sdsc.edu<http://= bioinformatics.sdsc.edu/>) at the San Diego Supercomputer Center (SDSC) (ht= tp://www.sdsc.edu<http://www.sdsc.edu/>) is involved in research and develo= pment activities centered around 3D structures of proteins and nucleic acid= s, the integration of structural data with other domains such as Medicine, = Genomics, Biology, Drug Discovery, and the development of scalable solution= to Big Data problems in Structural Bioinformatics. Our group leads the RCS= B Protein Data Bank (PDB) west-coast operations. The RCSB PDB (http://www.r= csb.org<http://www.rcsb.org/>) represents the preeminent source of experime= ntally determined macromolecular structure information for research and tea= ching in biology, biological chemistry, and medicine. With over 300,000 uni= que users from over 160 countries around the world, the RCSB PDB is one of = the leading worldwide Biological Databases. Our group is involved in the Na= tional Institutes of Health (NIH) Big Data to Knowledge (BD2K) initiative. As an Organized Research Unit of UC San Diego, SDSC is a world leader in da= ta-intensive computing and cyber infrastructure, providing resources, servi= ces, and expertise to the national research community, including industry a= nd academia. To apply, please send cover letter and resume to Dr. Peter Rose (pwrose@ucs= d.edu). -- Peter Rose, Ph.D. Site Head, RCSB Protein Data Bank West (http://www.rcsb.org<http://www.rcsb= .org/>) Principal Investigator, Structural Bioinformatics Laboratory (http://bioinf= ormatics.sdsc.edu<http://bioinformatics.sdsc.edu/>) San Diego Supercomputer Center (http://www.sdsc.edu<http://www.sdsc.edu/>) University of California, San Diego +1-858-822-5497<file://localhost/tel/%252B1-858-822-5497> --_000_D34D18B32D2C2pwroseucsdedu_ Content-Type: text/html; charset="Windows-1252" Content-ID: <[email protected]> Content-Transfer-Encoding: quoted-printable <html> <head> <meta http-equiv=3D"Content-Type" content=3D"text/html; charset=3DWindows-1= 252"> <meta name=3D"Title" content=3D""> <meta name=3D"Keywords" content=3D""> <meta name=3D"ProgId" content=3D"Word.Document"> <meta name=3D"Generator" content=3D"Microsoft Word 14"> <meta name=3D"Originator" content=3D"Microsoft Word 14"> <link 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mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:Cambria; mso-ascii-font-family:Cambria; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Cambria; mso-hansi-theme-font:minor-latin;} </style> <![endif]--><!--StartFragment--> <p class=3D"MsoNormal"><span style=3D"font-family:Arial">Summary: We are lo= oking for a highly motivated postdoc as part of our new project =93Compress= ive Structural Bioinformatics=94 funded by the US National Institutes of He= alth (NIH) Big Data to Knowledge (BD2K) initiative. <o:p></o:p></span></p> <p class=3D"MsoNormal"><span style=3D"font-family:Arial"> </span></p> <p class=3D"MsoNormal"><span style=3D"font-family:Arial">The Challenge: To = enable efficient research on the rapidly growing number of 3D molecular str= uctures of ever increasing size and complexity. Current algorithms used in = Structural Bioinformatics do not scale well with the rapid growth in structural data. In this project, we will em= ploy the latest advances in computer science to develop highly scalable, di= stributed parallel algorithms to overcome these limitations.<o:p></o:p></sp= an></p> <p class=3D"MsoNormal"><span style=3D"font-family:Arial"> </span></p> <p class=3D"MsoNormal"><span style=3D"font-family:Arial">Qualifications: Ph= .D. in one or more of the following research areas<o:p></o:p></span></p> <p class=3D"MsoListParagraphCxSpFirst" style=3D"text-indent:-.25in;mso-list= :l0 level1 lfo1"> <!--[if !supportLists]--><span style=3D"">=B7<span style=3D"font-size: 7pt;= font-family: 'Times New Roman';"> </span></span><!--[endif]--><span style=3D"font-family:Arial">Computer Scie= nce with a focus on large scale scientific computing<o:p></o:p></span></p> <p class=3D"MsoListParagraphCxSpMiddle" style=3D"text-indent:-.25in;mso-lis= t:l0 level1 lfo1"> <!--[if !supportLists]--><span style=3D"">=B7<span style=3D"font-size: 7pt;= font-family: 'Times New Roman';"> </span></span><!--[endif]--><span style=3D"font-family:Arial">Structural Bi= oinformatics with a focus on new methods development<o:p></o:p></span></p> <p class=3D"MsoListParagraphCxSpLast" style=3D"text-indent:-.25in;mso-list:= l0 level1 lfo1"> <!--[if !supportLists]--><span style=3D"">=B7<span style=3D"font-size: 7pt;= font-family: 'Times New Roman';"> </span></span><!--[endif]--><span style=3D"font-family:Arial">Computational= Structural Biology with a focus on improved structure solution methods<o:p= ></o:p></span></p> <p class=3D"MsoNormal"><span style=3D"font-family:Arial"> </span></p> <p class=3D"MsoNormal"><span style=3D"font-family:Arial">Experience with th= e development and performance optimization of scientific software. Demonstr= ated proficiency in a high-level programming language, such as Java or Pyth= on and experience with state of the art software development tools. Strong skills in applied mathematics and a= lgorithm design are required. High productivity demonstrated by publication= s and contributions to open source software projects. Experience in the dev= elopment and application of modern distributed parallel computing environments, such as Apache Big Data proje= cts including Apache Spark is a plus. Excellent interpersonal, written, and= oral presentation skills are essential.<o:p></o:p></span></p> <p class=3D"MsoNormal"><span style=3D"font-family:Arial"> </span></p> <p class=3D"MsoNormal"><span style=3D"font-family:Arial">Note, this positio= n is reviewed annually on the basis of performance and can be renewed for a= maximum of two years.<o:p></o:p></span></p> <p class=3D"MsoNormal"><span style=3D"font-family:Arial"> </span></p> <p class=3D"MsoNormal"><span style=3D"font-family:Arial">Our Environment:<o= :p></o:p></span></p> <p class=3D"MsoNormal"><span style=3D"font-family:Arial"> </span></p> <p class=3D"MsoNormal"><span style=3D"font-family:Arial">The Structural Bio= informatics Group (</span><a href=3D"http://bioinformatics.sdsc.edu/"><span= style=3D"font-family:Arial;color:#0000E9">http://bioinformatics.sdsc.edu</= span></a><span style=3D"font-family:Arial">) at the San Diego Supercomputer Center (SDSC) (</span><a href=3D"http://www= .sdsc.edu/"><span style=3D"font-family:Arial;color:#0000E9">http://www.sdsc= .edu</span></a><span style=3D"font-family:Arial">) is involved in research = and development activities centered around 3D structures of proteins and nucleic acids, the integration of structural= data with other domains such as Medicine, Genomics, Biology, Drug Discover= y, and the development of scalable solution to Big Data problems in Structu= ral Bioinformatics. Our group leads the RCSB Protein Data Bank (PDB) west-coast operations. The RCSB PDB (</sp= an><a href=3D"http://www.rcsb.org/"><span style=3D"font-family:Arial;color:= #0000E9">http://www.rcsb.org</span></a><span style=3D"font-family:Arial">) = represents the preeminent source of experimentally determined macromolecular structure information for research and teaching = in biology, biological chemistry, and medicine. With over 300,000 unique us= ers from over 160 countries around the world, the RCSB PDB is one of the le= ading worldwide Biological Databases. Our group is involved in the National Institutes of Health (NIH) Big Data = to Knowledge (BD2K) initiative.<o:p></o:p></span></p> <p class=3D"MsoNormal"><span style=3D"font-family:Arial"> </span></p> <p class=3D"MsoNormal"><span style=3D"font-family:Arial">As an Organized Re= search Unit of UC San Diego, SDSC is a world leader in data-intensive compu= ting and cyber infrastructure, providing resources, services, and expertise= to the national research community, including industry and academia.<o:p></o:p></span></p> <p class=3D"MsoNormal"><span style=3D"font-family:Arial"> </span></p> <p class=3D"MsoNormal"><span style=3D"font-family:Arial">To apply, please s= end cover letter and resume to Dr. Peter Rose ([email protected]).<o:p></o:p>= </span></p> <p class=3D"MsoNormal"><span style=3D"font-family:Arial"> </span></p> <p class=3D"MsoNormal"><span style=3D"font-family:Arial">--<o:p></o:p></spa= n></p> <p class=3D"MsoNormal"><span style=3D"font-family:Arial;color:#1A1A1A">Pete= r Rose, Ph.D.</span><span style=3D"font-family:Arial"><o:p></o:p></span></p= > <p class=3D"MsoNormal"><span style=3D"font-family:Arial;color:#1A1A1A">Site= Head, RCSB Protein Data Bank West (</span><a href=3D"http://www.rcsb.org/"= ><span style=3D"font-family:Arial;color:#103CC0">http://www.rcsb.org</span>= </a><span style=3D"font-family:Arial;color:#1A1A1A">)</span><span style=3D"= font-family:Arial"><o:p></o:p></span></p> <p class=3D"MsoNormal"><span style=3D"font-family:Arial">Principal Investig= ator, Structural Bioinformatics Laboratory (</span><a href=3D"http://bioinf= ormatics.sdsc.edu/"><span style=3D"font-family:Arial; color:#103CC0">http://bioinformatics.sdsc.edu</span></a><span style=3D"font= -family: Arial;color:#1A1A1A">)<o:p></o:p></span></p> <p class=3D"MsoNormal"><span style=3D"font-family:Arial;color:#1A1A1A">San = Diego Supercomputer Center (</span><a href=3D"http://www.sdsc.edu/"><span s= tyle=3D"font-family:Arial;color:#0000E9">http://www.sdsc.edu</span></a><spa= n style=3D"font-family:Arial;color:#1A1A1A">)</span><span style=3D"font-fam= ily:Arial"><o:p></o:p></span></p> <p class=3D"MsoNormal"><span style=3D"font-family:Arial;color:#3E003F">Univ= ersity of California, San Diego</span><span style=3D"font-family:Arial"><o:= p></o:p></span></p> <p class=3D"MsoNormal"><a href=3D"file://localhost/tel/%252B1-858-822-5497"= ><span style=3D"font-family:Arial;color:#103CC0">+1-858-822-5497</span>= </a><span style=3D"font-family:Arial"><o:p></o:p></span></p> <p class=3D"MsoNormal"><o:p> </o:p></p> <!--EndFragment--></div> </div> </div> </body> </html> --_000_D34D18B32D2C2pwroseucsdedu_-- --===============7552460431934394101== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline _______________________________________________ Biojava-l mailing list - [email protected] http://mailman.open-bio.org/mailman/listinfo/biojava-l --===============7552460431934394101==--