BioSimulators: a central registry of simulation engines and services for recommending specific tools.
BioSimulators: a central registry of simulation engines and services for recommending specific tools.
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DOI：
10.1093/nar/gkac331
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发表时间：
2022-07-05
影响因子：
14.9
通讯作者：
Karr, Jonathan R.
中科院分区：
文献类型：
--
作者：
Shaikh, Bilal;Smith, Lucian P.;Vasilescu, Dan;Marupilla, Gnaneswara;Wilson, Michael;Agmon, Eran;Agnew, Henry;Andrews, Steven S.;Anwar, Azraf;Beber, Moritz E.;Bergmann, Frank T.;Brooks, David;Brusch, Lutz;Calzone, Laurence;Choi, Kiri;Cooper, Joshua;Detloff, John;Drawert, Brian;Dumontier, Michel;Ermentrout, G. Bard;Faeder, James R.;Freiburger, Andrew P.;Frohlich, Fabian;Funahashi, Akira;Garny, Alan;Gennari, John H.;Gleeson, Padraig;Goelzer, Anne;Haiman, Zachary;Hasenauer, Jan;Hellerstein, Joseph L.;Hermjakob, Henning;Hoops, Stefan;Ison, Jon C.;Jahn, Diego;Jakubowski, Henry, V;Jordan, Ryann;Kalas, Matus;Koenig, Matthias;Liebermeister, Wolfram;Sheriff, Rahuman S. Malik;Mandal, Synchon;McDougal, Robert;Medley, J. Kyle;Mendes, Pedro;Mueller, Robert;Myers, Chris J.;Naldi, Aurelien;Nguyen, Tung V. N.;Nickerson, David P.;Olivier, Brett G.;Patoliya, Drashti;Pauleve, Loic;Petzold, Linda R.;Priya, Ankita;Rampadarath, Anand K.;Rohwer, Johann M.;Saglam, Ali S.;Singh, Dilawar;Sinha, Ankur;Snoep, Jacky;Sorby, Hugh;Spangler, Ryan;Starruss, Joern;Thomas, Payton J.;van Niekerk, David;Weindl, Daniel;Zhang, Fengkai;Zhukova, Anna;Goldberg, Arthur P.;Schaff, James C.;Blinov, Michael L.;Sauro, Herbert M.;Moraru, Ion I.;Karr, Jonathan R.
计算模型在促进生物科学、生物工程和医学方面具有巨大的潜力。然而，重现和重复使用模拟仍然具有挑战性，部分原因是用于模拟各种子系统和规模的各种格式和方法仍然被不同的软件工具孤立。例如，每个工具都必须通过不同的界面执行。为了帮助调查人员找到和使用模拟工具，我们开发了BioSimulator(https://biosimulators.org)，)，这是模拟工具功能的中央注册表，并为每个工具的每个版本提供一致的PYTHON、命令行和容器化界面。BioSimulator的基础是标准，如CellML、SBML、SED-ML和联合归档格式，以及模拟项目和模拟工具的验证工具，以确保这些标准得到一致使用。为了帮助建模师为特定项目找到工具，我们还使用注册表来开发推荐服务。我们预计BioSimulator将帮助建模人员交换、复制和组合模拟。BioSimulator通过抽象模拟项目和模拟工具来简化模拟。BioSimulator将项目抽象为将档案和工具组合为容器化的命令行界面。这些抽象使得对各种生物系统和尺度执行广泛的模拟变得更容易。
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various subsystems and scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find and use simulation tools, we developed BioSimulators (https://biosimulators.org), a central registry of the capabilities of simulation tools and consistent Python, command-line and containerized interfaces to each version of each tool. The foundation of BioSimulators is standards, such as CellML, SBML, SED-ML and the COMBINE archive format, and validation tools for simulation projects and simulation tools that ensure these standards are used consistently. To help modelers find tools for particular projects, we have also used the registry to develop recommendation services. We anticipate that BioSimulators will help modelers exchange, reproduce, and combine simulations. BioSimulators simplifies simulation by abstracting simulation projects and simulation tools. BioSimulators abstracts projects as COMBINE archives and tools as containerized command-line interfaces. These abstractions make it easier to execute a broad range of simulations for a variety of biological systems and scales.
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影响因子：
3
作者：
Bergmann FT;Adams R;Moodie S;Cooper J;Glont M;Golebiewski M;Hucka M;Laibe C;Miller AK;Nickerson DP;Olivier BG;Rodriguez N;Sauro HM;Scharm M;Soiland-Reyes S;Waltemath D;Yvon F;Le Novère N
通讯作者：
Le Novère N
影响因子：
9.9
作者：
Keating SM;Waltemath D;König M;Zhang F;Dräger A;Chaouiya C;Bergmann FT;Finney A;Gillespie CS;Helikar T;Hoops S;Malik-Sheriff RS;Moodie SL;Moraru II;Myers CJ;Naldi A;Olivier BG;Sahle S;Schaff JC;Smith LP;Swat MJ;Thieffry D;Watanabe L;Wilkinson DJ;Blinov ML;Begley K;Faeder JR;Gómez HF;Hamm TM;Inagaki Y;Liebermeister W;Lister AL;Lucio D;Mjolsness E;Proctor CJ;Raman K;Rodriguez N;Shaffer CA;Shapiro BE;Stelling J;Swainston N;Tanimura N;Wagner J;Meier-Schellersheim M;Sauro HM;Palsson B;Bolouri H;Kitano H;Funahashi A;Hermjakob H;Doyle JC;Hucka M;SBML Level 3 Community members
通讯作者：
SBML Level 3 Community members
模拟实验说明标记语言（SED-ML）：1级版本4的语言规范。
影响因子：
1.9
作者：
Smith LP;Bergmann FT;Garny A;Helikar T;Karr J;Nickerson D;Sauro H;Waltemath D;König M
通讯作者：
König M
DOI：
10.1109/tbme.2016.2560762
发表时间：
2016-10
期刊：
IEEE transactions on bio-medical engineering
影响因子：
--
作者：
Waltemath D;Karr JR;Bergmann FT;Chelliah V;Hucka M;Krantz M;Liebermeister W;Mendes P;Myers CJ;Pir P;Alaybeyoglu B;Aranganathan NK;Baghalian K;Bittig AT;Burke PE;Cantarelli M;Chew YH;Costa RS;Cursons J;Czauderna T;Goldberg AP;Gomez HF;Hahn J;Hameri T;Gardiol DF;Kazakiewicz D;Kiselev I;Knight-Schrijver V;Knupfer C;Konig M;Lee D;Lloret-Villas A;Mandrik N;Medley JK;Moreau B;Naderi-Meshkin H;Palaniappan SK;Priego-Espinosa D;Scharm M;Sharma M;Smallbone K;Stanford NJ;Song JH;Theile T;Tokic M;Tomar N;Toure V;Uhlendorf J;Varusai TM;Watanabe LH;Wendland F;Wolfien M;Yurkovich JT;Zhu Y;Zardilis A;Zhukova A;Schreiber F
通讯作者：
Schreiber F
影响因子：
19
作者：
Carrera J;Covert MW
通讯作者：
Covert MW