License

Knowledge base

The knowledge base sourcecode is licensed under MIT license.

CyanoFactory KB has been developed and further extended on the basis of WholeCellKB (Karr JR, Sanghvi JC, Macklin DN, Arora A, Covert MW.)

WholeCellKB: Model Organism Databases for Comprehensive Whole-Cell Models. Nucleic Acids Research 41, D787-D792 (2013). Nucleic Acids Research | PubMed, Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, Bolival B, Assad-Garcia N, Glass JI, Covert MW. A Whole-Cell Computational Model Predicts Phenotype from Genotype. Cell 150, 389-401 (2012). Cell | PubMed

MIT license

Copyright © 2012, Stanford University
Copyright © 2013-2016, Hochschule Mittweida, University of Applied Sciences

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Python package list

The Knowledge Base was developed using Python and the Webframework django.

  • biopython
  • django<1.9
  • django-celery (+RabbitMQ)
  • django-crispy-forms
  • django-dbarray
  • django-extensions
  • django-filter
  • django-guardian
  • django-haystack
  • django-jsonview
  • django-model-utils
  • django-widget-tweaks
  • djangorestframework
  • djangorestframework-xml
  • pyglpk (Patched Python3 version included in repository)
  • networkx
  • numpy
  • openpyxl
  • pillow
  • psycopg2 (+PostgreSQL)
  • pygraphviz>=1.3rc2
  • PyNetMet2 (shipped with CyanoFactory)
  • six
  • Wand
  • xapian-haystack (+Xapian)
  • xhtml2pdf

Design

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