Literature DB >> 17297480

Beyond standardization: dynamic software infrastructures for systems biology.

Morris A Swertz1, Ritsert C Jansen.   

Abstract

Progress in systems biology is seriously hindered by slow production of suitable software infrastructures. Biologists need infrastructure that easily connects to work that is done in other laboratories, for which standardization is helpful. However, the infrastructure must also accommodate the specifics of their biological system, but appropriate mechanisms to support variation are currently lacking. We argue that a minimal computer language, and a software tool called a generator, can be used to quickly produce customized software infrastructures that 'systems biologists really want to have'.

Mesh：

Year:  2007        PMID： 17297480     DOI： 10.1038/nrg2048

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN： 1471-0056            Impact factor:   53.242


  19 in total

Review 1.  Software for systems biology: from tools to integrated platforms.

Authors:  Samik Ghosh; Yukiko Matsuoka; Yoshiyuki Asai; Kun-Yi Hsin; Hiroaki Kitano
Journal:  Nat Rev Genet       Date:  2011-11-03       Impact factor: 53.242

Review 2.  Systems biology: perspectives on multiscale modeling in research on endocrine-related cancers.

Authors:  Robert Clarke; John J Tyson; Ming Tan; William T Baumann; Lu Jin; Jianhua Xuan; Yue Wang
Journal:  Endocr Relat Cancer       Date:  2019-06       Impact factor: 5.678

3.  The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button.

Authors:  Morris A Swertz; Martijn Dijkstra; Tomasz Adamusiak; Joeri K van der Velde; Alexandros Kanterakis; Erik T Roos; Joris Lops; Gudmundur A Thorisson; Danny Arends; George Byelas; Juha Muilu; Anthony J Brookes; Engbert O de Brock; Ritsert C Jansen; Helen Parkinson
Journal:  BMC Bioinformatics       Date:  2010-12-21       Impact factor: 3.169

4.  Towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics.

Authors:  Michael Gruenberger; Rudi Alberts; Damian Smedley; Morris Swertz; Paul Schofield; Klaus Schughart
Journal:  BMC Res Notes       Date:  2010-01-22

5.  SYSGENET: a meeting report from a new European network for systems genetics.

Authors:  Klaus Schughart
Journal:  Mamm Genome       Date:  2010-07-11       Impact factor: 2.957

6.  Mouse Resource Browser--a database of mouse databases.

Authors:  Michael Zouberakis; Christina Chandras; Morris Swertz; Damian Smedley; Michael Gruenberger; Jonathan Bard; Klaus Schughart; Nadia Rosenthal; John M Hancock; Paul N Schofield; George Kollias; Vassilis Aidinis
Journal:  Database (Oxford)       Date:  2010-07-06       Impact factor: 3.451

7.  designGG: an R-package and web tool for the optimal design of genetical genomics experiments.

Authors:  Yang Li; Morris A Swertz; Gonzalo Vera; Jingyuan Fu; Rainer Breitling; Ritsert C Jansen
Journal:  BMC Bioinformatics       Date:  2009-06-18       Impact factor: 3.169

8.  XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments.

Authors:  Morris A Swertz; K Joeri van der Velde; Bruno M Tesson; Richard A Scheltema; Danny Arends; Gonzalo Vera; Rudi Alberts; Martijn Dijkstra; Paul Schofield; Klaus Schughart; John M Hancock; Damian Smedley; Katy Wolstencroft; Carole Goble; Engbert O de Brock; Andrew R Jones; Helen E Parkinson; Ritsert C Jansen
Journal:  Genome Biol       Date:  2010-03-09       Impact factor: 13.583

9.  Comparative analysis of the human hepatic and adipose tissue transcriptomes during LPS-induced inflammation leads to the identification of differential biological pathways and candidate biomarkers.

Authors:  Ewa Szalowska; Martijn Dijkstra; Marieke G L Elferink; Desiree Weening; Marcel de Vries; Marcel Bruinenberg; Annemieke Hoek; Han Roelofsen; Geny M M Groothuis; Roel J Vonk
Journal:  BMC Med Genomics       Date:  2011-10-06       Impact factor: 3.063

10.  WormQTL--public archive and analysis web portal for natural variation data in Caenorhabditis spp.

Authors:  L Basten Snoek; K Joeri Van der Velde; Danny Arends; Yang Li; Antje Beyer; Mark Elvin; Jasmin Fisher; Alex Hajnal; Michael O Hengartner; Gino B Poulin; Miriam Rodriguez; Tobias Schmid; Sabine Schrimpf; Feng Xue; Ritsert C Jansen; Jan E Kammenga; Morris A Swertz
Journal:  Nucleic Acids Res       Date:  2012-11-24       Impact factor: 16.971
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