Welcome to Annotamentum’s Documentation.

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.

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.

Annot was developed using for browser the firefox developer edition. However, all major browsers are supported.

Source code is available under GNU AGPLv3 license. This manual is written under the GNU FDLv1.3 license.

This are links to source code and a poster presentation at PyCon 2015 Montreal, Canada at the very beginning of project.

This user manual: is structured in tutorial, how-tos, reference and discussion.

• Tutorial
  • Preparation
  • Controlled Vocabulary
  • Bricks
    • Upload the Bricks to make them accessible in the Experiment Layout Layer!
  • Investigations and Studies
  • Experiment Layouts
  • Assay and Superset generation Tracking
  • Backup your Work
• HowTos
  • Annot
    • HowTo install annot?
    • HowTo json files and youe web browser?
    • HowTo set up an additional annot user?
    • HowTo fire up annot?
    • HowTo enter annot?
    • HowTo get files from your host machine into annot?
    • HowTo get files from inside annot to your hostmachine?
    • HowTo list all available commands?
    • HowTo backup annot content?
    • HowTo backup acpipeTemplateCode_*.py code?
    • HowTo fix anjson annotation that propagates from the acaxis to the superset to the runset layer?
    • HowTo handle controlled vocabulary?
    • HowTo deal with huge ontologies?
    • HowTo get detailed information about the ontologies in use?
    • HowTo handle bricks?
    • HowTo annotate protein complexes?
    • Howto make bricks accessible in the experiment layout layer?
    • HowTo layout experiments?
    • HowTo disable the date tracking app?
    • HowTo handle study and investigation?
  • Django
    • Howto enable the django-debug-toolbar?
  • Docker
    • HowTo install the docker platform?
    • HowTo run the docker platform?
  • PostgreSQL
    • HowTo enter the postgresql database?
• Reference
  • Annot workflow
  • Docker and how the annot folder is structured
  • The nginx and nginxdev folder
  • The dbdata folder
  • The web, webdev and fsdata folder
    • Python3
    • acJson - the assay coordinate json file format
    • Django
    • The folder structure inside the annot/web/ folder
  • The man folder
• Discussion
  • Why Annot?
  • About Controlled Vocabulary
  • About Proteins, Protein Isoforms, and Protein Complexes
  • About not_yet_specified and not_available
  • Programmer Contribution
  • Contact Information
• GNU Free Documentation License