Reproducible Research Using Biomodels

被引:13
作者
Mendes, Pedro [1 ,2 ]
机构
[1] Univ Connecticut, Sch Med, Ctr Quantitat Med, Farmington, CT 06030 USA
[2] Univ Connecticut, Sch Med, Dept Cell Biol, Farmington, CT 06030 USA
关键词
Reproducibility; Biomodels; Standards; SYSTEMS BIOLOGY; MARKUP LANGUAGE; MODELS; EXCHANGE;
D O I
10.1007/s11538-018-0498-z
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
Like other types of computational research, modeling and simulation of biological processes (biomodels) is still largely communicated without sufficient detail to allow independent reproduction of results. But reproducibility in this area of research could easily be achieved by making use of existing resources, such as supplying models in standard formats and depositing code, models, and results in public repositories.
引用
收藏
页码:3081 / 3087
页数:7
相关论文
共 35 条
  • [1] Baker M, 2016, NATURE, V533, P452, DOI 10.1038/533452a
  • [2] CHANCE B, 1960, J BIOL CHEM, V235, P2426
  • [3] BioModels: ten-year anniversary
    Chelliah, Vijayalakshmi
    Juty, Nick
    Ajmera, Ishan
    Ali, Raza
    Dumousseau, Marine
    Glont, Mihai
    Hucka, Michael
    Jalowicki, Gael
    Keating, Sarah
    Knight-Schrijver, Vincent
    Lloret-Villas, Audald
    Natarajan, Kedar Nath
    Pettit, Jean-Baptiste
    Rodriguez, Nicolas
    Schubert, Michael
    Wimalaratne, Sarala M.
    Zhao, Yangyang
    Hermjakob, Henning
    Le Novere, Nicolas
    Laibe, Camille
    [J]. NUCLEIC ACIDS RESEARCH, 2015, 43 (D1) : D542 - D548
  • [4] Claerbout J.F., 1992, ELECT DOCUMENTS GIVE, P601, DOI [10.1190/1.1822162, DOI 10.1190/1.1822162]
  • [5] SBRML: a markup language for associating systems biology data with models
    Dada, Joseph O.
    Spasic, Irena
    Paton, Norman W.
    Mendes, Pedro
    [J]. BIOINFORMATICS, 2010, 26 (07) : 932 - 938
  • [6] GENERAL METHOD FOR NUMERICALLY SIMULATING STOCHASTIC TIME EVOLUTION OF COUPLED CHEMICAL-REACTIONS
    GILLESPIE, DT
    [J]. JOURNAL OF COMPUTATIONAL PHYSICS, 1976, 22 (04) : 403 - 434
  • [7] NeuroML: A Language for Describing Data Driven Models of Neurons and Networks with a High Degree of Biological Detail
    Gleeson, Padraig
    Crook, Sharon
    Cannon, Robert C.
    Hines, Michael L.
    Billings, Guy O.
    Farinella, Matteo
    Morse, Thomas M.
    Davison, Andrew P.
    Ray, Subhasis
    Bhalla, Upinder S.
    Barnes, Simon R.
    Dimitrova, Yoana D.
    Silver, R. Angus
    [J]. PLOS COMPUTATIONAL BIOLOGY, 2010, 6 (06) : 1 - 19
  • [8] What does research reproducibility mean?
    Goodman, Steven N.
    Fanelli, Daniele
    Ioannidis, John P. A.
    [J]. SCIENCE TRANSLATIONAL MEDICINE, 2016, 8 (341)
  • [9] Structuring supplemental materials in support of reproducibility
    Greenbaum, Dov
    Rozowsky, Joel
    Stodden, Victoria
    Gerstein, Mark
    [J]. GENOME BIOLOGY, 2017, 18
  • [10] Guerreiro Maria., 2017, Forking software used in eLife papers to GitHub