diff --git a/INSTALLATION.md b/INSTALLATION.md index 7f0d7559..8081126c 100644 --- a/INSTALLATION.md +++ b/INSTALLATION.md @@ -7,7 +7,7 @@ To setup the development server the following minimal requirements must be fulfilled - `docker` - `docker-compose` -- `Python3.6` +- `Python3.8` For elasticsearch the following system settings are required ``` diff --git a/README.md b/README.md index f2628421..7122b710 100644 --- a/README.md +++ b/README.md @@ -13,7 +13,6 @@ and * [Funding](https://github.com/matthiaskoenig/pkdb#funding) ## Overview -[[^]](https://github.com/matthiaskoenig/pkdb#pk-db---a-pharmacokinetics-database) [PK-DB](https://pk-db.com) is a database and web interface for pharmacokinetics data and information from clinical trials as well as pre-clinical research. PK-DB allows to curate pharmacokinetics data integrated with the corresponding meta-information @@ -29,16 +28,13 @@ Important features are - a workflow for collaborative data curation - strong validation rules on data, and simple access via a REST API -PK-DB is available at https://pk-db.com +PK-DB is available at https://pk-db.com and https://alpha.pk-db.com. The terms of use are listed in the [`TERMS_OF_USE.md`](./TERMS_OF_USE.md). + +![PK-DB overview](./docs/images/data_extraction.png) ## How to cite -[[^]](https://github.com/matthiaskoenig/pkdb#pk-db---a-pharmacokinetics-database) If you use PK-DB data or the web interface cite -> *PK-DB: PharmacoKinetics DataBase for Individualized and Stratified Computational Modeling* -> Jan Grzegorzewski, Janosch Brandhorst, Dimitra Eleftheriadou, Kathleen Green, Matthias König -> bioRxiv 760884; doi: https://doi.org/10.1101/760884 - > Grzegorzewski J, Brandhorst J, Green K, Eleftheriadou D, Duport Y, Barthorscht F, Köller A, Ke DYJ, De Angelis S, König M. > *PK-DB: pharmacokinetics database for individualized and stratified computational modeling*. > Nucleic Acids Res. 2020 Nov 5:gkaa990. doi: [10.1093/nar/gkaa990](https://doi.org/10.1093/nar/gkaa990). Epub ahead of print. PMID: [33151297](https://pubmed.ncbi.nlm.nih.gov/33151297/). @@ -48,15 +44,16 @@ If you use PK-DB code cite in addition [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1406979.svg)](https://doi.org/10.5281/zenodo.1406979) ## License -[[^]](https://github.com/matthiaskoenig/pkdb#pk-db---a-pharmacokinetics-database) PK-DB code and documentation is licensed as * Source Code: [LGPLv3](http://opensource.org/licenses/LGPL-3.0) * Documentation: [CC BY-SA 4.0](http://creativecommons.org/licenses/by-sa/4.0/) ## Funding -[[^]](https://github.com/matthiaskoenig/pkdb#pk-db---a-pharmacokinetics-database) Jan Grzegorzewski and Matthias König are supported by the Federal Ministry of Education and Research (BMBF, Germany) within the research network Systems Medicine of the Liver ([LiSyM](http://www.lisym.org/), grant number 031L0054). +Matthias König is supported by the German Research Foundation (DFG) within the Research Unit Programme FOR 5151 +[QuaLiPerF](https://qualiperf.de) (Quantifying Liver Perfusion-Function Relationship in Complex Resection - +A Systems Medicine Approach) by grant number 436883643 and by grant number +465194077 (Priority Programme SPP 2311, Subproject SimLivA). - -© 2017-2020 Jan Grzegorzewski & Matthias König; https://livermetabolism.com. +© 2017-2022 Jan Grzegorzewski & Matthias König; https://livermetabolism.com. diff --git a/docker-compose-production.yml b/docker-compose-production.yml index 86126886..9c10fb51 100644 --- a/docker-compose-production.yml +++ b/docker-compose-production.yml @@ -36,6 +36,8 @@ services: - "5433:5432" volumes: - postgres_data:/var/lib/postgresql/data + env_file: + - .env.production environment: - POSTGRES_DB=${PKDB_DB_NAME} - POSTGRES_USER=${PKDB_DB_USER} diff --git a/release-notes/0.9.6.md b/release-notes/0.9.6.md new file mode 100644 index 00000000..b133db02 --- /dev/null +++ b/release-notes/0.9.6.md @@ -0,0 +1,14 @@ +# Release notes for pkdb 0.9.6 +We are pleased to release the next version of PK-DB including the +following changes: + +- django security bugfix, update dependency 3.2.0 (#713, #722) +- support for geometric means (#677, #686) +- removed name from reference json (#688) +- updated backend dependencies +- better encoding of multiple dosing (#685) +- updated acknowledgements (#714) +- fixing backend errors on non-existing queries +- updated README + +Your PK-DB team \ No newline at end of file