Projects: pypi: BOFdat
https://packages.ecosyste.ms/registries/pypi.org/packages/BOFdat
Package to generate biomass objective function stoichiometric coefficients from experimental data
7 versions
Latest release: almost 6 years ago
17 downloads last month
Enhanced Analysis
Educational Contributors:
[email protected]
[email protected]
Repository Activity:
Repository Owner:
Jean-Christophe Lachance (user)
PhD candidate, Bioinformatics, Université de Sherbrooke. My research focuses on the Systems Biology of minimal cells. Academic
PhD candidate, Bioinformatics, Université de Sherbrooke. My research focuses on the Systems Biology of minimal cells. Academic
README Analysis:
DOI Found
Science Score: 100/100
Starting Score: 100 points
Bonuses:
-
+40
Educational commit emails
2 contributors with educational email addresses -
+20
Academic repository owner
Repository owned by academic institution -
+4
Science terms in README
2 scientific terms found in README -
+10
DOI references
1 DOI references found in README
Penalties:
-
-10
PyPI ecosystem
General-purpose ecosystem -
-15
No science keywords
No scientific terms found in keywords/classifiers
Very Likely Science (100)
Papers Mentioning BOFdat 11
10.1371/journal.pcbi.1006644
A computational knowledge-base elucidates the response of Staphylococcus aureus to different media typesCited by: 35
Author(s): Yara Seif, Jonathan M. Monk, Nathan Mih, Hannah Tsunemoto, Saugat Poudel, Cristal Zuñiga, Jared T. Broddrick, Karsten Zengler, Jaehyung Kim
Software Mentions: 7
Published: over 6 years ago
10.3390/metabo11040232
First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple AuxotrophiesCited by: 7
Author(s): Alina Renz, Lina Widerspick, Andreas Dräger
Software Mentions: 4
Published: over 4 years ago
10.1186/s13059-021-02289-z
Addressing uncertainty in genome-scale metabolic model reconstruction and analysisCited by: 55
Author(s): David B Bernstein, Snorre Sulheim, Eivind Almaas, Daniel Segrè
Software Mentions: 4
Published: over 4 years ago
10.15252/msb.202010099
Genome‐scale metabolic modeling reveals key features of a minimal gene setCited by: 12
Author(s): Jean-Christophe Lachance, Dominick Matteau, Joëlle Brodeur, Colton J. Lloyd, Nathan Mih, Zachary A. King, Thomas F. Knight, Adam M. Feist, Jonathan M. Monk, Jaehyung Kim, Pierre-Étienne Jacques, Sébastien Rodrigue
Software Mentions: 2
Published: about 4 years ago
10.3389/fgene.2020.00116
Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic PathogenCited by: 9
Author(s): Christian Salgård Jensen, Charles J. Norsigian, Xin Fang, Xiaohui Chen Nielsen, Jens Jørgen Christensen, Bernhard Ø. Palsson, Jonathan M. Monk
Software Mentions: 2
Published: over 5 years ago
10.3390/metabo11080491
Modelling hCDKL5 Heterologous Expression in BacteriaCited by: 5
Author(s): Marco Fondi, Stefano Gonzi, Mikołaj Dziurzyński, Paola Turano, Veronica Ghini, Marzia Calvanese, Andrea Colarusso, Concetta Lauro, Ermenegilda Parrilli, Maria Luisa Tutino
Software Mentions: 2
Published: about 4 years ago
10.1186/s12896-021-00702-w
Genome-scale insights into the metabolic versatility of Limosilactobacillus reuteriCited by: 6
Author(s): Hao Luo, Peishun Li, Hao Wang, Stefan Roos, Boyang Ji, Jens Nielsen
Software Mentions: 2
Published: almost 4 years ago
10.1039/d0mo00154f
Mechanistic models of microbial community metabolismCited by: 13
Author(s): Lillian Dillard, Dawson Payne, Jason A. Papin
Software Mentions: 2
Published: over 4 years ago
10.1038/s41598-020-69509-7
Genome-scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediationCited by: 17
Author(s): Shany Ofaim, Raphy Zarecki, Seema Porob, Daniella Gat, Tamar Lahav, Yechezkel Kashi, Radi Aly, Hanan Eizenberg, Zeev Ronen, Shiri Freilich
Software Mentions: 1
Published: almost 5 years ago
10.1371/journal.pcbi.1006971
BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental dataCited by: 69
Author(s): Jean-Christophe Lachance, Colton J. Lloyd, Jonathan M. Monk, Laurence T. Yang, Anand V. Sastry, Yara Seif, Jaehyung Kim, Sébastien Rodrigue, Adam M. Feist, Zachary A. King, Pierre-Étienne Jacques
Software Mentions: 1
Published: over 6 years ago
10.3389/fbioe.2021.602464
Strategies for Enhancing in vitro Degradation of Linuron by Variovorax sp. Strain SRS 16 Under the Guidance of Metabolic ModelingCited by: 5
Author(s): Kusum Dhakar, Raphy Zarecki, Daniella van Bommel, Nadav Knossow, Shlomit Medina, Başak Öztürk, Radi Aly, Hanan Eizenberg, Zeev Ronen, Shiri Freilich
Software Mentions: 1
Published: over 4 years ago