- User's guide: browsing and searching simulations
- Developer's guide: Installing your own WholeCellSimDB server and storing simulations
- Need help?
- Development team
- Citing WholeCellSimDB
See wholecell.org for additional information about whole-cell models.## User's guide: browsing and searching simulations See the online [user's guide](http://www.wholecellsimdb.org/help). ## Developer's guide: Installing your own WholeCellSimDB server and storing simulations See the online [developers's guide](http://www.wholecellsimdb.org/help) for installation instructions including a list of required packages and instructions for integreating WholeCellSimDB with whole-cell models. ## Need help? Please contact the development team at [firstname.lastname@example.org](mailto:email@example.com). ## Implementation WholeCellSimDB is a hybrid SQL/HDF database implemented in [Python](http://www.python.org/). The [Django](https://www.djangoproject.com/) framework was used to construct a [MySQL](http://www.mysql.org) database containing simulation metadata as well as links to HDF files containing the simulation predictions. The [H5py](http://www.h5py.org/) package was used to read and write HDF files. Full text search over the simulation metadata was implemented using [Xapian](http://xapian.org/) and [Haystack](http://haystacksearch.org/). The web interface was run using [Apache](http://httpd.apache.org/) and [mod_wsgi](https://code.google.com/p/modwsgi/). The web interface was developed using [flot](http://www.flotcharts.org/), [Google Fonts](https://www.google.com/fonts), [jQuery](http://jquery.com/), [jqTree](http://mbraak.github.io/jqTree), [jQWidgets](http://www.jqwidgets.com/), and [FamFamFam Silk icons](http://www.famfamfam.com/lab/icons/silk/). ## Development team WholeCellSimDB was developed by researchers at Mount Sinai School of Medicine, Stanford University, and the University of Prince Edward Island. * [Jonathan Karr](http://research.mssm.edu/karr), Mount Sinai School of Medicine * [Nolan Phillips](http://ca.linkedin.com/pub/nolan-phillips/68/935/702), University of Prince Edward Island * [Markus Covert](http://covertlab.stanford.edu), Stanford University ## Citing WholeCellSimDB Please see the following for more information or to cite WholeCellSimDB: * Karr JR et al. WholeCellSimDB: hybrid HDF/SQL database for whole-cell model predictions. (In preparation). * 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](http://www.cell.com/abstract/S0092-8674(12)00776-3) | [PubMed](http://www.ncbi.nlm.nih.gov/pubmed/22817898) ## The MIT License (MIT)
Copyright © 2013-2014 Covert Lab, Stanford University
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