title: COSMOS: Python library for massively parallel workflows.
abstract: CONCLUSIONS
  Efficient workflows to shepherd clinically generated genomic data through the multiple stages of a next-generation sequencing pipeline are of critical importance in translational biomedical science. Here we present COSMOS, a Python library for workflow management that allows formal description of pipelines and partitioning of jobs. In addition, it includes a user interface for tracking the progress of jobs, abstraction of the queuing system and fine-grained control over the workflow. Workflows can be created on traditional computing clusters as well as cloud-based services.
  
  
  METHODS
  Source code is available for academic non-commercial research purposes. Links to code and documentation are provided at http://lpm.hms.harvard.edu and http://wall-lab.stanford.edu.
  
  
  BACKGROUND
  dpwall@stanford.edu or peter_tonellato@hms.harvard.edu.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors: Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA and Department of Biology, Mohammed V University-Agal, 4 Ibn Battouta Avenue, Rabat B.P:1014RP, Morocco.
authors: Erik
authors: E
authors: Gafni
authors: Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA and Department of Biology, Mohammed V University-Agal, 4 Ibn Battouta Avenue, Rabat B.P:1014RP, Morocco.
authors: Lovelace J
authors: LJ
authors: Luquette
authors: Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA and Department of Biology, Mohammed V University-Agal, 4 Ibn Battouta Avenue, Rabat B.P:1014RP, Morocco Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA and Department of Biology, Mohammed V University-Agal, 4 Ibn Battouta Avenue, Rabat B.P:1014RP, Morocco.
authors: Alex K
authors: AK
authors: Lancaster
authors: Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA and Department of Biology, Mohammed V University-Agal, 4 Ibn Battouta Avenue, Rabat B.P:1014RP, Morocco.
authors: Jared B
authors: JB
authors: Hawkins
authors: Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA and Department of Biology, Mohammed V University-Agal, 4 Ibn Battouta Avenue, Rabat B.P:1014RP, Morocco.
authors: Jae-Yoon
authors: JY
authors: Jung
authors: Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA and Department of Biology, Mohammed V University-Agal, 4 Ibn Battouta Avenue, Rabat B.P:1014RP, Morocco Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA and Department of Biology, Mohammed V University-Agal, 4 Ibn Battouta Avenue, Rabat B.P:1014RP, Morocco.
authors: Yassine
authors: Y
authors: Souilmi
authors: Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA and Department of Biology, Mohammed V University-Agal, 4 Ibn Battouta Avenue, Rabat B.P:1014RP, Morocco Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA and Department of Biology, Mohammed V University-Agal, 4 Ibn Battouta Avenue, Rabat B.P:1014RP, Morocco.
authors: Dennis P
authors: DP
authors: Wall
authors: Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA and Department of Biology, Mohammed V University-Agal, 4 Ibn Battouta Avenue, Rabat B.P:1014RP, Morocco Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA and Department of Biology, Mohammed V University-Agal, 4 Ibn Battouta Avenue, Rabat B.P:1014RP, Morocco.
authors: Peter J
authors: PJ
authors: Tonellato
mesh_terms: D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D011381:Programming Languages