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marsi

Metabolite Analogues for Strain Improvement

https://github.com/biosustain/marsi

Science Score: 28.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 3 committers (66.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.4%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

Metabolite Analogues for Strain Improvement

Basic Info
  • Host: GitHub
  • Owner: biosustain
  • License: apache-2.0
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 168 MB
Statistics
  • Stars: 0
  • Watchers: 11
  • Forks: 2
  • Open Issues: 0
  • Releases: 0
Created over 9 years ago · Last pushed over 7 years ago
Metadata Files
Readme License Citation

README.md

marsi - Metabolite Analogues for Rational Strain Improvement

Build Status

marsi is an open-source software to created to identify non-GMO strain design targets

Dependencies

  • eigen3 >= 3.0
  • OpenBabel >= 2.2.3
  • RDKit >= 2016
  • glpk
  • cplex (optional)
  • Cython >= 0.25
  • numpy >= 1.11

Quick Start

  1. Install the Dependencies
  2. pip install marsi
  3. Run marsi --help from the command line

More details in Quick Start

Initialization

marsi comes with a initialization command that will download all the necessary files and build the database. You can start by running marsi db --help.

marsi will download the required files for you, setup the database and process the molecular structures. Just run marsi db init. Make sure you have an stable internet connection.

Documentation

Complete documentation can be found at https://biosustain.github.io/marsi.

License

Apache License Version 2.0

Databases and Software Tools

All tools and databases are listed here

Owner

  • Name: DTU Biosustain
  • Login: biosustain
  • Kind: organization
  • Location: Denmark

The Novo Nordisk Foundation Center for Biosustainability

Citation (CITATIONS.md) 

Citations
---------

Papers for databases and software tools used in this work.

## Databases

### PDSP Ki DATABASE
1. The Multiplicity of Serotonin Receptors: Uselessly diverse molecules or an embarrasment of riches? BL Roth, WK Kroeze, S Patel and E Lopez: The Neuroscientist, 6:252-262, 2000
2. Science Netwatch, {28 January 2000; 287 (5453)}.

### Zinc
3. Irwin, Sterling, Mysinger, Bolstad and Coleman, J. Chem. Inf. Model. 2012 DOI: 10.1021/ci3001277. 
4. Irwin and Shoichet, J. Chem. Inf. Model. 2005;45(1):177-82

### ChEBI
5. Hastings, J., de Matos, P., Dekker, A., Ennis, M., Harsha, B., Kale, N., Muthukrishnan, V., Owen, G., Turner, S., Williams, M., and Steinbeck, C. (2013) The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res.

### PubChem
6. Kim S, Thiessen PA, Bolton EE, Chen J, Fu G, Gindulyte A, Han L, He J, He S, Shoemaker BA, Wang J, Yu B, Zhang J, Bryant SH. PubChem Substance and Compound databases. Nucleic Acids Res. 2016 Jan 4; 44(D1):D1202-13. Epub 2015 Sep 22 doi: 10.1093/nar/gkv951

### DrugBank
7. Law V, Knox C, Djoumbou Y, Jewison T, Guo AC, Liu Y, Maciejewski A, Arndt D, Wilson M, Neveu V, Tang A, Gabriel G, Ly C, Adamjee S, Dame ZT, Han B, Zhou Y, Wishart DS. DrugBank 4.0: shedding new light on drug metabolism. Nucleic Acids Res. 2014 Jan 1;42(1):D1091-7.

### KEGG
8. Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M., and Tanabe, M.; KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 44, D457-D462 (2016).
9. Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000).

### BiGG
10. Zachary A. King, Justin Lu, Andreas Dräger, Philip Miller, Stephen Federowicz, Joshua A. Lerman, Ali Ebrahim, Bernhard O. Palsson, and Nathan E. Lewis BiGG Models: A platform for integrating, standardizing and sharing genome-scale models Nucl. Acids Res. (04 January 2016) 44 (D1): D515-D522 first published online October 17, 2015 doi:10.1093/nar/gkv1049

### BindingDB
11. Tiqing Liu, Yuhmei Lin, Xin Wen, Robert N. Jorissen, and Michael K. Gilson BindingDB: a web-accessible database of experimentally determined protein–ligand binding affinities Nucleic Acids Res. 2007 Jan; 35(Database issue): D198–D201. Published online 2006 Dec 1. doi:  10.1093/nar/gkl999

## Solubility
12. Delaney, J. S. (2004). ESOL: Estimating aqueous solubility directly from molecular structure. Journal of Chemical Information and Computer Sciences, 44(3), 1000–1005. http://doi.org/10.1021/ci034243x

## Software Tools

## COBRApy
13. Ebrahim A, Lerman JA, Palsson BO, Hyduke DR (2013) COBRApy: COnstraints-Based Reconstruction and Analysis for Python. BMC Syst Biol 7: 74. Available: http://www.biomedcentral.com/1752-0509/7/74.

## Cameo
14. Computer-aided metabolic engineering and optimization; https://cameo.bio

### OpenBabel
15. Noel M O'Boyle, Michael Banck, Craig A James, Chris Morley, Tim Vandermeersch and Geoffrey R Hutchison Open Babel: An open chemical toolbox Journal of Cheminformatics 20113:33 DOI:10.1186/1758-2946-3-33

### RDKit
14. RDKit: Open-source cheminformatics; http://www.rdkit.org

GitHub Events

Total
Last Year

Committers

Last synced: over 3 years ago

All Time
  • Total Commits: 482
  • Total Committers: 3
  • Avg Commits per committer: 160.667
  • Development Distribution Score (DDS): 0.006
Top Committers
Name Email Commits
Joao Cardoso j****a@b****k 479
João Gonçalo Rocha Cardoso j****o@g****m 2
Nikolaus Sonnenschein n****o@b****k 1
Committer Domains (Top 20 + Academic)
biosustain.dtu.dk: 2

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Packages

  • Total packages: 1
  • Total downloads:
    • pypi 14 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 5
  • Total maintainers: 1
pypi.org: marsi

marsi - Metabolite Analogues for Rational Strain Improvement

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 14 Last month
Rankings
Dependent packages count: 10.1%
Forks count: 19.2%
Dependent repos count: 21.6%
Average: 27.7%
Stargazers count: 38.8%
Downloads: 48.6%
Maintainers (1)
Joo.Cardoso
Last synced: 11 months ago