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Literature DB >> 22048662

Software for systems biology: from tools to integrated platforms.

Samik Ghosh¹, Yukiko Matsuoka, Yoshiyuki Asai, Kun-Yi Hsin, Hiroaki Kitano.

Abstract

Understanding complex biological systems requires extensive support from software tools. Such tools are needed at each step of a systems biology computational workflow, which typically consists of data handling, network inference, deep curation, dynamical simulation and model analysis. In addition, there are now efforts to develop integrated software platforms, so that tools that are used at different stages of the workflow and by different researchers can easily be used together. This Review describes the types of software tools that are required at different stages of systems biology research and the current options that are available for systems biology researchers. We also discuss the challenges and prospects for modelling the effects of genetic changes on physiology and the concept of an integrated platform.

Mesh：

Year: 2011 PMID： 22048662 DOI： 10.1038/nrg3096

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

99 in total

1. KEGG: kyoto encyclopedia of genes and genomes.

Authors: M Kanehisa; S Goto
Journal: Nucleic Acids Res Date: 2000-01-01 Impact factor: 16.971

2. Regulation of noise in the expression of a single gene.

Authors: Ertugrul M Ozbudak; Mukund Thattai; Iren Kurtser; Alan D Grossman; Alexander van Oudenaarden
Journal: Nat Genet Date: 2002-04-22 Impact factor: 38.330

Review 3. Standards for systems biology.

Authors: Alvis Brazma; Maria Krestyaninova; Ugis Sarkans
Journal: Nat Rev Genet Date: 2006-08 Impact factor: 53.242

Review 4. The minimum information about a proteomics experiment (MIAPE).

Authors: Chris F Taylor; Norman W Paton; Kathryn S Lilley; Pierre-Alain Binz; Randall K Julian; Andrew R Jones; Weimin Zhu; Rolf Apweiler; Ruedi Aebersold; Eric W Deutsch; Michael J Dunn; Albert J R Heck; Alexander Leitner; Marcus Macht; Matthias Mann; Lennart Martens; Thomas A Neubert; Scott D Patterson; Peipei Ping; Sean L Seymour; Puneet Souda; Akira Tsugita; Joel Vandekerckhove; Thomas M Vondriska; Julian P Whitelegge; Marc R Wilkins; Ioannnis Xenarios; John R Yates; Henning Hermjakob
Journal: Nat Biotechnol Date: 2007-08 Impact factor: 54.908

5. Therapeutically targeting ErbB3: a key node in ligand-induced activation of the ErbB receptor-PI3K axis.

Authors: Birgit Schoeberl; Emily A Pace; Jonathan B Fitzgerald; Brian D Harms; Lihui Xu; Lin Nie; Bryan Linggi; Ashish Kalra; Violette Paragas; Raghida Bukhalid; Viara Grantcharova; Neeraj Kohli; Kip A West; Magdalena Leszczyniecka; Michael J Feldhaus; Arthur J Kudla; Ulrik B Nielsen
Journal: Sci Signal Date: 2009-06-30 Impact factor: 8.192

6. Inferring the transcriptional network of Bacillus subtilis.

Authors: Abeer Fadda; Ana Carolina Fierro; Karen Lemmens; Pieter Monsieurs; Kristof Engelen; Kathleen Marchal
Journal: Mol Biosyst Date: 2009-07-28

7. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data.

Authors: J S Edwards; R U Ibarra; B O Palsson
Journal: Nat Biotechnol Date: 2001-02 Impact factor: 54.908

Review 8. Reconstruction of biochemical networks in microorganisms.

Authors: Adam M Feist; Markus J Herrgård; Ines Thiele; Jennie L Reed; Bernhard Ø Palsson
Journal: Nat Rev Microbiol Date: 2008-12-31 Impact factor: 60.633

9. The BioPAX community standard for pathway data sharing.

Authors: Emek Demir; Michael P Cary; Suzanne Paley; Ken Fukuda; Christian Lemer; Imre Vastrik; Guanming Wu; Peter D'Eustachio; Carl Schaefer; Joanne Luciano; Frank Schacherer; Irma Martinez-Flores; Zhenjun Hu; Veronica Jimenez-Jacinto; Geeta Joshi-Tope; Kumaran Kandasamy; Alejandra C Lopez-Fuentes; Huaiyu Mi; Elgar Pichler; Igor Rodchenkov; Andrea Splendiani; Sasha Tkachev; Jeremy Zucker; Gopal Gopinath; Harsha Rajasimha; Ranjani Ramakrishnan; Imran Shah; Mustafa Syed; Nadia Anwar; Ozgün Babur; Michael Blinov; Erik Brauner; Dan Corwin; Sylva Donaldson; Frank Gibbons; Robert Goldberg; Peter Hornbeck; Augustin Luna; Peter Murray-Rust; Eric Neumann; Oliver Ruebenacker; Oliver Reubenacker; Matthias Samwald; Martijn van Iersel; Sarala Wimalaratne; Keith Allen; Burk Braun; Michelle Whirl-Carrillo; Kei-Hoi Cheung; Kam Dahlquist; Andrew Finney; Marc Gillespie; Elizabeth Glass; Li Gong; Robin Haw; Michael Honig; Olivier Hubaut; David Kane; Shiva Krupa; Martina Kutmon; Julie Leonard; Debbie Marks; David Merberg; Victoria Petri; Alex Pico; Dean Ravenscroft; Liya Ren; Nigam Shah; Margot Sunshine; Rebecca Tang; Ryan Whaley; Stan Letovksy; Kenneth H Buetow; Andrey Rzhetsky; Vincent Schachter; Bruno S Sobral; Ugur Dogrusoz; Shannon McWeeney; Mirit Aladjem; Ewan Birney; Julio Collado-Vides; Susumu Goto; Michael Hucka; Nicolas Le Novère; Natalia Maltsev; Akhilesh Pandey; Paul Thomas; Edgar Wingender; Peter D Karp; Chris Sander; Gary D Bader
Journal: Nat Biotechnol Date: 2010-09-09 Impact factor: 54.908

Review 10. A comprehensive map of the mTOR signaling network.

Authors: Etienne Caron; Samik Ghosh; Yukiko Matsuoka; Dariel Ashton-Beaucage; Marc Therrien; Sébastien Lemieux; Claude Perreault; Philippe P Roux; Hiroaki Kitano
Journal: Mol Syst Biol Date: 2010-12-21 Impact factor: 11.429

107 in total

1. Bioinformatics: Next-generation omics.

Authors: Tanita Casci
Journal: Nat Rev Genet Date: 2012-05-02 Impact factor: 53.242

Review 2. Systems Biology for Smart Crops and Agricultural Innovation: Filling the Gaps between Genotype and Phenotype for Complex Traits Linked with Robust Agricultural Productivity and Sustainability.

Authors: Anil Kumar; Rajesh Kumar Pathak; Sanjay Mohan Gupta; Vikram Singh Gaur; Dinesh Pandey
Journal: OMICS Date: 2015-10

Software for systems biology: from tools to integrated platforms.

1. KEGG: kyoto encyclopedia of genes and genomes.

2. Regulation of noise in the expression of a single gene.

Review 3. Standards for systems biology.

Review 4. The minimum information about a proteomics experiment (MIAPE).

5. Therapeutically targeting ErbB3: a key node in ligand-induced activation of the ErbB receptor-PI3K axis.

6. Inferring the transcriptional network of Bacillus subtilis.

7. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data.

Review 8. Reconstruction of biochemical networks in microorganisms.

9. The BioPAX community standard for pathway data sharing.

Review 10. A comprehensive map of the mTOR signaling network.

1. Bioinformatics: Next-generation omics.

Review 2. Systems Biology for Smart Crops and Agricultural Innovation: Filling the Gaps between Genotype and Phenotype for Complex Traits Linked with Robust Agricultural Productivity and Sustainability.

3. A Survey of DICOM Viewer Software to Integrate Clinical Research and Medical Imaging.

Review 4. Systems biology: perspectives on multiscale modeling in research on endocrine-related cancers.

Review 5. Systems-level analysis of innate immunity.

6. Derivative-Free Optimization of Rate Parameters of Capsid Assembly Models from Bulk in Vitro Data.

Review 7. Plant metabolic modeling: achieving new insight into metabolism and metabolic engineering.

Review 8. Next-generation proteomics: towards an integrative view of proteome dynamics.

Review 9. Technical note: proteomic approaches to fundamental questions about neutrophil biology.

Review 10. How many molecular subtypes? Implications of the unique tumor principle in personalized medicine.