echinopscis

echinopscis is an experiment on creating an “extensible notebook for open science on specimens”. We’re a group of biodiversity & informatics researchers trying to make it easier to access the information resources (specimens, literature, descriptions) needed to describe and protect biodiversity. We want to enable flexible working practices, so that researchers can collate and publish work with actionable links to evidence. This effort is part of the groundwork towards the “digital extended specimen”.

Phase 1 is a prototype desktop working environment for biodiversity researchers. This simplifies data access, annotation and linking, supporting published and working hypotheses. Researchers can search data from authoritative sources, store it locally and create links. Data classes currently include literature, specimens, names, institutions, people and traits. (If something you need is missing, then please tell us.)

Our key design principles are:

• Control of your data. As a researcher, you remain in complete control of your data. Your data is stored in open, text format, on your local machine. It will always be accessible in the future without any need for specialised software.
• Open to choose your working practices. We’ve extended an existing, well-documented working environment - Obsidian. We’ve provided subject specific functions: search, retrieval, annotation and linking of key resources. These are aimed at biodiversity researchers, to enable work with:
  • Scientific names
  • Specimens
  • Literature resources
  • People
  • Institutions
    You can use these to combine your data and working notes in many different ways. Your workflow is your own to decide - you are “open to choose” how to organise your work.
• Re-usable skills. You may need to learn some new skills to work with this toolkit. We aim that these will always be an investment: transferable to other tools and practices. These include things like markdown formatting, bibliography / citation management and document production. They can also be applied elsewhere in your work, or in other working environments.
• Open science. All code and documentation (and this project site) are managed on github. Contributions of all kinds are welcome. We’re currently participating in the Open Life Sciences mentoring and training program. We aim to use open science practices to open the management of this project. We want to build an inclusive and sustainable community.

Overview presentation

Try it out

Follow the installation instructions