As one of the requirements of my internship at InterMine through the Outreachy organization, I have to write bi-weekly blog posts about my project and overall internship progress. I will dedicate this post to shed some light on the InterMine open-source project and my work for them.
What is InterMine?
InterMine is an open-source data warehouse that integrates biological data from a variety of sources. It allows researchers to analyze and search available data through a web-based user interface. InterMine was developed by the Micklem lab at the University of Cambridge with the Wellcome Trust's support; complementary projects have been funded by the National Human Genome Research Institute (NIH/NHGRI) and the Biotechnology and Biological Sciences Research Council (BBSRC).
There's an InterMine for (almost) anyone!
There are many different InterMines worldwide, covering a broad range of model organisms and life science research areas, including but not limited to:
- FlyMine - a data warehouse of integrated fruit fly genetic, genomic and proteomic data
- HumanMine - an integrated database of Homo sapiens genomic data
- MouseMine - an integrated data warehouse of mouse genomic data, developed by MGI
- YeastMine - an integrated data warehouse of yeast genomic data, developed by SGD
- ZebrafishMine - an integrated data warehouse of zebrafish genomic data, developed by ZFIN
- RatMine - an integrated data warehouse of rat genomic data, developed by RGD
For the full list of InterMines, please see the registry.
The problem
User manuals and tutorials are provided to assist users in efficiently finding their desired information. The user documentation and tutorials currently focus mainly on the InterMine’s legacy UI that will be replaced by another new interface called BlueGenes. The new user interface will have the same features as the older one; however, there is a considerable difference in appearance and some functionality differences. These changes will cause the current user documents and videos to be incompatible with the BlueGenes interface, confusing users while looking for information. Consequently, all user training documents and videos should be re-created based on the BlueGenes interface. The updated user documents will be in the form of short videos with captions and voice-over, written user manuals with screenshots, and exercises and answers sections.
My role
My role is to recreate and modify the user training documents and videos based on the new BlueGenes interface, which will help users learn how to use the various features the new UI offers. The process will involve working with mentors and the InterMine team to:
- Choose a particular theme that will be consistent through all of the documentation and videos.
- Explore the current user documentation to get style or format inspiration
- Use the BlueGenes UI’s different sections to get familiar with its features and abilities.
- Work on writing the text first as it can be a good starting point for videos (text can be used as a script for videos). Creating written tutorials also helps acquire hands-on experience on how things are done on the interface.
- Create videos whenever applicable to explain advanced and more complex functionalities.
- All work should move from the more straightforward tasks to advanced ones
- If time permits, create documentation for particular biological use-cases - cookbook documentation
Technology Stack
During my first week as an intern, I had the chance to explore different tools to complete my tasks. I had a discussion with my mentors to select specific technologies to be used in the project, including:
- GitBook to create the documentation site; all documents will be written in Markdown.
- GIMP to edit all screenshots and images included in the documentation.
- Camtasia to create videos.
I hope you enjoyed reading about my project; stay tuned for more posts about my internship journey!