.. Annotamentum documentation master file, created by sphinx-quickstart on Wed Apr 26 12:14:35 2017. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. Welcome to Annotamentum's Documentation. ======================================== .. image:: img/annotlogo06.png :height: 128 :alt: An! official annot logo :align: center *Django admin based sample, reagent and experiment metadata tracking.* **Summary:** `Annot`_ is a web application, developed for biological wetlab experiment layout, sample and reagent logging, so that data is ready for sharing and analysis. On its core annot makes use of the `acpipe_anjson`_ library and acjson - assay coordinate `json`_ - file format. The use of controlled vocabulary from ontologies for sample and reagent annotation is enforced. Annot's modular implementation can be adapted to a variety of experimental paradigms. .. _Annot: https://gitlab.com/biotransistor/annot .. _acpipe_anjson: https://gitlab.com/biotransistor/acpipe_acjson .. _json: http://json.org/ **Implementation:** The annot web application is implemented in python3 utilizing roughly `django`_, `postgresql`_, `nginx`_. Annot is deployed via `docker`_ container platform. Annot code it self is thereby packed into a `debian`_ docker container. .. _django: https://www.djangoproject.com/ .. _postgresql: https://www.postgresql.org/ .. _nginx: https://nginx.org/ .. _docker: https://www.docker.com/ .. _debian: https://www.debian.org/ Annot was developed using for browser the `firefox`_ developer edition. However, all major browsers are supported. .. _firefox: https://www.mozilla.org/en-US/firefox/developer/ Source code is available under `GNU AGPLv3`_ license. This manual is written under the `GNU FDLv1.3`_ license. .. _GNU AGPLv3: https://www.gnu.org/licenses/licenses.html#AGPL .. _GNU FDLv1.3: https://www.gnu.org/licenses/licenses.html#FDL This are **links** to `source code`_ and a `poster presentation`_ at PyCon 2015 Montreal, Canada at the very beginning of project. .. _source code: https://gitlab.com/biotransistor/annot .. _poster presentation: https://us.pycon.org/2015/schedule/presentation/461/ .. _publication: https://www.youtube.com/watch?v=dQw4w9WgXcQ **This user manual:** is structured in tutorial, how-tos, reference and discussion. .. toctree:: :maxdepth: 3 man_tutorial man_howto man_reference man_discussion fdl-1_3