Affiliation: University of Manchester
- Systematic integration of experimental data and models in systems biologyPeter Li
School of Chemistry, The University of Manchester, Manchester M13 9PL, UK
BMC Bioinformatics 11:582. 2010..Automating the assembly and use of systems biology models is dependent upon data integration processes involving the interoperation of data and analytical resources...
- Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially-expressed genes from microarray dataPeter Li
Manchester Centre for Integrative Systems Biology and School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess St, Manchester, M1 7DN, UK
BMC Bioinformatics 9:334. 2008..Furthermore, this transfer of data may require a reconciliation step in order for there to be interoperability between computational tools...
- Automated manipulation of systems biology models using libSBML within Taverna workflowsPeter Li
School of Chemistry and Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, UK
Bioinformatics 24:287-9. 2008..The ability of Taverna to invoke Java classes and methods is demonstrated by a workflow in which we use libSBML to map gene expression data onto a metabolic pathway represented as a SBML model...
- myExperiment: a repository and social network for the sharing of bioinformatics workflowsCarole A Goble
School of Computer Science, The University of Manchester, Manchester M13 9PL, UK
Nucleic Acids Res 38:W677-82. 2010..Further documentation about myExperiment including its REST web service is available from http://wiki.myexperiment.org. Feedback and requests for support can be sent to firstname.lastname@example.org...
- Taverna: a tool for building and running workflows of servicesDuncan Hull
School of Computer Science, University of Manchester, M13 9PL, UK
Nucleic Acids Res 34:W729-32. 2006..These high-level workflows can integrate many different resources into a single analysis. Taverna is available freely under the terms of the GNU Lesser General Public License (LGPL) from http://taverna.sourceforge.net/...
- Growth control of the eukaryote cell: a systems biology study in yeastJuan I Castrillo
Faculty of Life Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK
J Biol 6:4. 2007..Comprehensive studies at the transcriptional, proteomic and metabolic levels under defined controlled conditions are currently lacking...
- Bridging the gap between in silico and cell-based analysis of the nuclear factor-kappaB signaling pathway by in vitro studies of IKK2Adaoha E C Ihekwaba
School of Chemistry, The University of Manchester, Faraday Building, UK
FEBS J 274:1678-90. 2007..Hence, interpretation of in silico models should be made in the context of this uncertainty...
- Biosphere: the interoperation of web services in microarray cluster analysisKei Hoi Cheung
Center for Medical Informatics, Yale University, 300 George Street, New Haven, CT 06511, USA
Appl Bioinformatics 3:253-6. 2004....
- An efficient and high-throughput approach for experimental validation of novel human gene predictionsPius M Brzoska
Applied Biosystems, 850 Lincoln Center Drive, Foster City, CA 94404, USA
Genomics 87:437-45. 2006..Reevaluation of these transcripts produced 574 novel transcripts using RefSeq as a reference. RT-PCR sequencing in combination with RACE on ab initio gene predictions could be used to define the transcriptome across all species...
- Taverna: a tool for the composition and enactment of bioinformatics workflowsTom Oinn
EMBL European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
Bioinformatics 20:3045-54. 2004..A growing number of these resources are being made available with programmatic access in the form of Web services. Bioinformatics scientists will need to orchestrate these Web services in workflows as part of their analyses...
- Systematic identification of pseudogenes through whole genome expression evidence profilingAlison Yao
Celera Genomics, 45 West Gude Dr, Rockville, MD 20850, USA
Nucleic Acids Res 34:4477-85. 2006..We have demonstrated the power of whole genome profiling of expression sequences to improve the accuracy of gene annotations...
- Gene and alternative splicing annotation with AIRLiliana Florea
Informatics Research, Applied Biosystems, Rockville, Maryland 20850, USA
Genome Res 15:54-66. 2005....
- The Celera Discovery SystemAnthony Kerlavage
Celera Genomics, 45 W Gudd Drive, Rockville, MD 20850, USA
Nucleic Acids Res 30:129-36. 2002..A user workspace keeps track of queries and analyses. CDS is widely used by the academic research community and requires a subscription for access. The system and academic pricing information are available at http://cds.celera.com...