title: CoreFlow: a computational platform for integration, analysis and modeling of complex biological data.
abstract: A major challenge in mass spectrometry and other large-scale applications is how to handle, integrate, and model the data that is produced. Given the speed at which technology advances and the need to keep pace with biological experiments, we designed a computational platform, CoreFlow, which provides programmers with a framework to manage data in real-time. It allows users to upload data into a relational database (MySQL), and to create custom scripts in high-level languages such as R, Python, or Perl for processing, correcting and modeling this data. CoreFlow organizes these scripts into project-specific pipelines, tracks interdependencies between related tasks, and enables the generation of summary reports as well as publication-quality images. As a result, the gap between experimental and computational components of a typical large-scale biology project is reduced, decreasing the time between data generation, analysis and manuscript writing. CoreFlow is being released to the scientific community as an open-sourced software package complete with proteomics-specific examples, which include corrections for incomplete isotopic labeling of peptides (SILAC) or arginine-to-proline conversion, and modeling of multiple/selected reaction monitoring (MRM/SRM) results.
  
  
  CONCLUSIONS
  CoreFlow was purposely designed as an environment for programmers to rapidly perform data analysis. These analyses are assembled into project-specific workflows that are readily shared with biologists to guide the next stages of experimentation. Its simple yet powerful interface provides a structure where scripts can be written and tested virtually simultaneously to shorten the life cycle of code development for a particular task. The scripts are exposed at every step so that a user can quickly see the relationships between the data, the assumptions that have been made, and the manipulations that have been performed. Since the scripts use commonly available programming languages, they can easily be transferred to and from other computational environments for debugging or faster processing. This focus on 'on the fly' analysis sets CoreFlow apart from other workflow applications that require wrapping of scripts into particular formats and development of specific user interfaces. Importantly, current and future releases of data analysis scripts in CoreFlow format will be of widespread benefit to the proteomics community, not only for uptake and use in individual labs, but to enable full scrutiny of all analysis steps, thus increasing experimental reproducibility and decreasing errors. This article is part of a Special Issue entitled: Can Proteomics Fill the Gap Between Genomics and Phenotypes?
authors: Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
authors: Adrian
authors: A
authors: Pasculescu
authors: Cellular Signal Integration Group (C-SIG), Center for Biological Sequence Analysis (CBS), Department of Systems Biology, Technical University of Denmark (DTU), Building 301, DK-2800, Lyngby, Denmark.
authors: Erwin M
authors: EM
authors: Schoof
authors: Cellular Signal Integration Group (C-SIG), Center for Biological Sequence Analysis (CBS), Department of Systems Biology, Technical University of Denmark (DTU), Building 301, DK-2800, Lyngby, Denmark.
authors: Pau
authors: P
authors: Creixell
authors: Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
authors: Yong
authors: Y
authors: Zheng
authors: Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
authors: Marina
authors: M
authors: Olhovsky
authors: Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
authors: Ruijun
authors: R
authors: Tian
authors: Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada; Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.
authors: Jonathan
authors: J
authors: So
authors: Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Department of Cardiac Surgery, University of Toronto, Ontario, Canada.
authors: Rachel D
authors: RD
authors: Vanderlaan
authors: Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
authors: Tony
authors: T
authors: Pawson
authors: Cellular Signal Integration Group (C-SIG), Center for Biological Sequence Analysis (CBS), Department of Systems Biology, Technical University of Denmark (DTU), Building 301, DK-2800, Lyngby, Denmark. Electronic address: linding@cbs.dtu.dk.
authors: Rune
authors: R
authors: Linding
authors: Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada. Electronic address: colwill@lunenfeld.ca.
authors: Karen
authors: K
authors: Colwill
mesh_terms: D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D013058:Mass Spectrometry / Q000379:methods; D011381:Programming Languages; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software; D057188:Workflow
keywords: Computational pipeline; Data analysis; Mass spectrometry; Statistical analysis; Workflow