#SAPLING: sapling.cshl.edu
![alt text][logo] [logo]: https://github.com/wimverleyen/SAPLING/blob/master/logo/saplingoriglogo.png "SAPLING"
Web application to perform gene network analysis
amqp (1.4.6) anyjson (0.3.3) ballotbox (0.1) BeautifulSoup (3.2.0) billiard (3.3.0.18) biopython (1.59) celery (3.1.16) Cython (0.20.2) decorator (3.4.0) distribute (0.6.21) Django (1.8.2) django-braces (1.4.0) django-bulk-update (1.1.3) django-celery (3.1.16) django-celery-with-redis (3.0) django-crispy-forms (1.4.0) django-debug-toolbar (1.2.1) django-selectable (0.9.0) docopt (0.6.2) freetype-py (1.0) gdbn (0.1) gnumpy (0.2) HTSeq (0.6.1) joblib (0.7.0d) jsonschema (0.5) keggrest (0.1.1) kombu (3.0.23) matplotlib (1.2.0) matplotlib-venn (0.2) mock (1.0.1) mpi4py (1.3) MySQL-python (1.2.5) networkx (1.9.1) nolearn (0.3.1) nose (1.3.4) numexpr (2.4) numpy (1.9.1) nxpydot (0.1) pandas (0.15.2) patsy (0.3.0) PIL (1.1.7) pip (1.5.6) psycopg2 (2.4.5) pydot (1.0.28) pydotplus (2.0.2) pyparsing (2.0.3) python-dateutil (2.4.0) pytz (2014.7) PyYAML (3.10) redis (2.10.3) reportlab (2.5) rpy2 (2.3.5) scikit-learn (0.16.1) scipy (0.9.0) seaborn (0.5.1) setuptools (3.6) six (1.8.0) sqlparse (0.1.13) statsmodels (0.5.0) storm (0.19) tables (2.3.1) Theano (0.6.0rc3) virtualenv (1.11.6) wsgiref (0.1.2) zope.deprecation (4.1.2) zope.event (4.0.2) zope.interface (4.0.5)
This is the main directory for SAPLING. Typically, settings, templates, forms, URLs, etc. related to the Django are programmed.
The directory of the gene function prediction (GFP) application collects all the code for the models, views, forms, URLs, etc. Also, the tasks for computing a GFP and aggregation are situated in this directory. These tasks bind to a celery defined name and will be scheduled accordingly.
A factory design pattern is used to implement the machine learning algorithms. Furthermore, loading the appropriate data for the network analysis, communication with the underlying MySQL database, the performance evaluation, the execution of the aggregation of different types of network analysis, etc. are implemented in this directory.
The implementation of the enrichment analysis can be found in this directory. The enrichment analysis is not configured as a separate application in the Django framework.
The Python module reportlab is used to generate a portable document format (pdf) of all the network analyses performed by SAPLING.