menoci logo

Welcome to menoci.io

menoci is a collection of open source Drupal extension modules that can be used to rapidly deploy an integrated website and data management portal for research projects in the biomedical and life sciences.

The menoci modules have are actively developed and maintained by the University Medical Center Göttingen, Department of Medical Informatics, and Scientific Data Center Göttingen, GWDG.

Architecture

Based on the Drupal web content management system, menoci introduces multiple extension modules that support scientific data management for life science research projects.

Schematic representation of the menoci system architecture.

Features

Features of menoci include:

  • Manage and display the scientific track record of your project in a standardized format (peer-reviewed article, published datasets, preprints, etc.)
  • Document and display all resources linked to the published data
  • Keep track of key assets for your biomedical experiments:
    • Antibodies,
    • Mouse lines and mice,
    • Cell lines* and cell models (iPSC, hiPSC)
    • Laboratory notebooks*
  • Store your research data in CDSTAR and publish datasets with persistent resolvable identifiers from the ePIC consortium.

*) The menoci modules "Cell Model Catalogue" and "Lab Notebook Registry" are not currently included in the default software distribution but are freely available upon request.

Reference projects

ProjectDescriptionDuration
CRC 1002The project investigates heart insufficiency in translational medicine. Origin of the menoci software.2012 - today
CRC 1190Compartmental Gates and Contact Sites in Cells. more information2014 - today
CRC 1286The project is specialised in Quantitative Synaptology and promotes a modern infrastructure including super-resolution imaging facilities. more information2017 - today

Literature

The menoci software project has been covered in the following scientific articles:

  • Suhr M, Lehmann C, Bauer CR, Bender T, Knopp C, Freckmann L, et al. menoci: Lightweight Extensible Web Portal enabling FAIR Data Management for Biomedical Research Projects. Feb 2020, arXiv:200206161. PREPRINT
  • Lehmann C, Suhr M, Umbach N, Cyganek L, Kleinsorge M, Nussbeck SY, et al. Leaving spreadsheets behind – FAIR documentation and representation of human stem cell lines in the Collaborative Research Centre 1002. GMDS 2019, Dortmund. doi:10.3205/19gmds037.
  • Rheinländer S, Aschenbrandt G, Nussbeck SY, Suhr M, Kusch H. Towards standardized documentation of mouse lines in biomedical basic research. GMDS 2019, Dortmund. doi:10.3205/19gmds038.
  • Suhr M, Jahn N, Mietchen D, Kusch H. Wikidata as semantic representation platform of the scientific achievements of the biomedical Collaborative Research Centre 1002. GMDS 2018, Osnabrück. doi:10.3205/18gmds173.
  • Kusch H, Schmitt O, Marzec B, Nussbeck SY. Data organization of a clinical Collaborative Research Center in an integrated, long-term accessible Research Data Platform. GMDS 2015, Krefeld. doi:10.3205/15gmds104.

Contact

This project is currently maintained by


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Introduction

menoci is a collection of Drupal extension modules that can be used to rapidly deploy an integrated website and data management portal for research projects in the biomedical and life sciences.

The menoci modules are actively developed and maintained by the University Medical Center Göttingen, Department of Medical Informatics, and Göttingen Scientific Data Center, GWDG.

menoci Source Code

The menoci suite is distributed via the dedicated menoci GitLab repository.

Original Repositories

This distribution repository comprises the following menoci modules:

  • Commons: shared libraries, group and subproject handling
  • Data Archive: store and share data packages (using CDSTAR as a backend storage service; https://gitlab.gwdg.de/cdstar/cdstar)
  • Literature: publication list
  • Wikidata: optional extension of the publication list, that cross-references Wikidata pages of registered articles
  • Antibody Catalogue: track antibodies used in the project
  • Mouse Line Catalogue: track mouse lines and specimen used in the project

License

Website/Documentation

This documentation is created with mdbook.

The source code of this website is available at menoci-docs GitLab Repository

menoci Project

Copyright (C) 2012-2020 menoci contributors, see AUTHORS.md

The menoci project source code is licensed under GNU General Public License 3.0, see license file

Documentation

This documentation is licensed under Creative Commons license CC-BY-SA 4.0 unless otherwise stated.

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Download

Get the latest version from our public distribution GitLab Repository.

Releases

The following official distribution release versions of the menoci project are available:

VersionDateDOIComment
1.02020-02-05doi:10.25625/NC9TF6Initial menoci release

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Installation

On any Linux-based host system with docker and docker-compose packages installed: Get the latest menoci release version, for example by cloning the official Gitlab repository:

  • git clone https://gitlab.gwdg.de/medinfpub/menoci.git
  • cd menoci to enter the new directory

For a quick exploration, build a Docker image from the shipped Dockerfile:

  • docker build -t local/menoci .
  • docker run -p 80:80 --name menoci local/menoci
  • Open localhost in web browser, proceed with Drupal installation (choose SQLite database since no other database is available for this container)

More permanent installation should be done via docker-compose.yml with command docker-compose up -d:
preferably to path /opt/docker/menoci

version: '2.0'

services:

  drupal:
    build: . # Build local image
    ports:
      - 80:80
    volumes:
      - sites:/var/www/html/sites

  database:
    image: mariadb
    volumes:
      - mysql:/var/lib/mysql
    environment:
      MYSQL_RANDOM_ROOT_PASSWORD: "yes"
      MYSQL_DATABASE: drupal
      MYSQL_USER: menoci
      MYSQL_PASSWORD: ChangeIt

volumes:
  sites:
  mysql:

When using docker-compose.yml file to orchestrate webserver and database containers, be sure to correctly map the database service name from the compose file to database hostname during Drupal installation:

Database configuration

Database choice

  • Installation with MySQL/MariaDB as a database server is recommenced.
  • SQLite may be a valid choice for testing purposes but some Drupal database mapping may diverge between engines.
  • Only MySQL/MariaDB is tested and validated by the development team.

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Configuration

After installing Drupal and the menoci modules, some basic settings have to be configured through the Drupal administration user interface.

Configuration instructions on this page are currently work in progress.

Modules

Navigate your browser to the route admin/modules/ of your Drupal instance.

  1. Enable "jQuery Update" module

Appearance

Go to admin/appearance/

  1. Enable "Bootstrap" theme and set as default.

  2. [optional] In Bootstrap settings, "Advanced": set "CDN provider" to "custom" and replace default paths (like https://cdn.jsdelivr.net/npm/bootstrap@3.4.1/dist/*) with
    /sites/all/libraries/bootstrap. The result should look like this for the the first CSS parameter:
    /sites/all/libraries/bootstrap/css/bootstrap.css
    respectively for the CSS and JS fields. (This is optional but Bootstrap library files are shipped with the default Docker container, allowing you to minimize CDN traffic and related user tracking.)

Bootstrap theme configuration

Modules

Go to admin/modules/

  1. Enable "Commons" module, press "save" button, and confirm that module dependencies will be automatically installed.
  2. Enable "Publication Registry" module.
  3. Choose from the following optional menoci modules to install:
    • Mouseline Catalogue
    • Research Data Archive
    • Wikidata extension
Configuration

Go to admin/config/

  1. Create first research group
  2. [optional] Create subprojects

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Roadmap

Development of menoci is actively pursued at the Göttingen Department of Medical Informatics. Please find below a rough outline of future release versions and features to expect.

The menoci project roadmap is subject to change. If you would like to see certain features implemented on schedule, feel free to contact us and contribute to development.

Version 1.1, June 2020

  • Node Link Extension: a new prototype module will be included that enables integration of configurable Drupal content types into the menoci Published Data Registry. Arbitrary data types can be integrated as additional "Catalogues" without the need to write actual source code.

Version 1.2, July 2020

  • Antibody Catalogue:
    • JSON-LD Support: Extending JSON to JSON-LD to enhance linked data functionality.
    • Automated PID Generation: Migrate from pre-registered PIDs to automated generation of PIDs.
  • Mouseline Catalogue:
    • JSON-LD Support: Extending JSON to JSON-LD to enhance linked data functionality.
    • Automated PID Generation: Migrate from pre-registered PIDs to automated generation of PIDs.
    • Traceability: Add features to track creators and editors of Mouseline Catalogue contents.

Later releases, tdb.

  • Advanced Light Microscopy and Nanoscopy (ALMN): The ALMN module provides workflow support and data management functionality for imaging facilities. The public release version will feature fully configurable project branding options.
    • Initial publication of generic module version
  • Lab Notebook registry: The Lab Notebook Registry provides users with the option to create a digital representation of their orginal paper notebooks used for primary experimental documentation at the bench.
    • Automated PID Generation: Migrate from pre-registered PIDs to automated generation of PIDs
  • Cell Model Catalogue:
    • Initial publication of generic module version
    • JSON-LD Support: Extending JSON to JSON-LD to enhance linked data functionality.
  • Drupal Major Version Upgrade: Migration from Drupal 7 to a recent release version.
  • Dissemination and Development: First steps are already taken to further disseminate menoci among the scientific community and to spread the development among multiple stakeholders.
    • Extend development processes to other stakeholders
  • Dataverse Integration: Allow upload of research data into Dataverse for long-term preservation and DOI registration.

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Privacy policy

The menoci.io web site is run by the University Medical Center Göttingen, Department of Medical Infomatics.

When this policy refers to “we”, this means the above Department of Medical Informatics.

We strictly limit the processing of your personal information, and in general process as little data as possible to fulfill our mission. We won't sell your data to any third party.

Whom to contact

If you have questions please contact mi@med.uni-goettingen.de.


This privacy policy has been adapted from the FSFE website


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Imprint

University Medical Center Göttingen
Department of Medical Informatics

Prof. Dr. Dagmar Krefting
Head of Department

Robert-Koch-Str. 40
37075 Göttingen, Germany

E-Mail: mi@med.uni-goettingen.de
Phone: +49 551 39-3431


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