How to Set up a Chemistry Networks Project

Summary of Project Infrastructure

You will need to use:

Some means of sharing all your work - the details. This is typically an online Lab Notebook. It's essential that all the detail can be seen without having to sign in - that the work is Googleable. Sometimes contributors from the private sector may need to keep some details back. Everyone understands this, but all contributors must at all times maximise disclosure. You can use any online lab notebook. SGC Open Chemistry Networks have an agreement with Labarchives (LA) that means you can use LA to record all your work. It's then easy to link from Github to your ELN.
Github, used for discussions and updates. Github is used for more human-friendly summaries and discussions. It is also used for hosting useful files, but it's no substitute for a lab notebook.
The Living Paper, for the most comprehensive "story so far" and the route to clearly defined authorship.
A compound registration system, to keep track of all the molecules in the project and their associated data. This is being set up now.
Social Media, for outreach.

Understand the Rules and the Need for Leadership

For a description of the general idea, read the Six Laws of Open Source Drug Discovery. The most important ideas are that all data and ideas are freely shared (in as near to real time as possible), anyone may participate and there will be no patents. There is a FAQs page for the Chemistry Networks Projects and more detailed T&Cs.

Open projects are built around communities of people who want to contribute. Some people will contribute a lot, some much less. A core of the project will be funded, but many contributions will come pro bono. Either way, expect the need for leadership. A person, or people, will need to be in charge. That position comes not from some given "authority" but through being the most active contributor or coordinator. If a project lacks leadership, it's likely it won't go very far or very fast. But the leader can change. The leader of one project can be different from the leader of another, and the leader can be you.

Establish the Project Team

The core team and the extended community are both crucial. The core will involve people who are expected to be heavily invested in the project longer term. They will include the researchers who are contributing the original data, for example, and interested members of those teams. These are like the "founders" and should be listed on the front page (the "readme") of the relevant repository along with affiliations and their Github user ID's so that everyone knows who's who.

In addition, for each project, there needs to be a Sir James Murray Student Champion and a Pharma Industry Champion. These roles are described in full on separate pages (see the wiki menu). In short, the student champion is a junior researcher who is responsible for project management. The pharma champion is a part-time strategic consultant.

Everything in all these projects will be openly available on Github, including all the shared files. To contribute, however, (i.e. to write things or add files) people will need to be added to Structural Genomics Consortium Github list of people, which is very easy to do.

Github Basics

First thing: get a Github account. It's not spammy, and you can control how you get email alerts to new content. Send your username to your project's Student Champion or to chemistry@thesgc.org so that you can be added to the project and then you will be able to write things.

Each project takes place in a Github repository (you're looking at one now), which will need creating for new projects. There is a separate page on repositories in this wiki (see the menu on the right), but ultimately each SGC Open Chemistry Networks Project has a URL like github.com/StructuralGenomicsConsortium/(the short name of the project.)

You can read about where projects are up to on the wiki. You can read what people are talking about in the Issues.

But you will be asking "How do I do things?" Github is unusual in that almost everything is editable. On most pages it's possible to click an "edit" button and see how people are doing things. There is also a very large amount of help available online, which you can usually most easily find by Googling your problem. There are also lots of existing contributors who can help you.

If you want to ask a question, start an "Issue" - give it a title and write what you want. It can be a question, or it can be an FYI for example. If you want to attract someone's attention, "tag" them (i.e. put the "@" and their username). If you want to add a comment on someone else's issue, go right ahead.

You'll notice that on the main page of each repository (the "code" tab) there's a bunch of files shown. People have uploaded these. You can add folders and files much like you do on your own computer. This is a good way to share files with everyone. If you want to do this like a pro, you can download the desktop Github app and sync what's online with what's on your computer.

Set Up The Living Paper

Each project should be accompanied by a living paper that provides the most accurate, concise and readable "story so far".

Set up a Google Doc with a permissions level that allows anyone with the link to edit. Copy the shareable link, then use tinyurl to create a short version of the URL that looks like tinyurl.com/SGC-CNPX where X is the number of the project you're starting. In the Google Doc set up the initial text to look like this:

This document is a living version of the paper describing the SGC Chemical Networks Project X (name of the Github project) and is the most up to date version of the paper. The URL for this page is (link) This document is editable. Upon milestones being reached a snapshot will be taken and the snapshot submitted as a preprint. The online project hub is (link). FAQs are here. Title
Author List
Abstract
Paper Body
Current Priority Action Items (5 or 10)
References
Acknowledgements
Link to SI document (this is a new Google doc) and the filestore (a folder on Github for files associated with the paper).

The idea behind the living paper is described in full here (link needed). In short: preprints are posted (which are snapshots of the living paper) at the beginning of the project, when key progress is made, and at the end of the project. The aim of the preprints is to provide a Story So Far, and to clarify who has contributed to the project sufficiently to warrant authorship. It is expected that the initial and final preprints would be peer-reviewed and independently published as papers in an open access journal.

Talk to People!

There are lots of people already involved in Chemistry Networks Projects who can advise how they work. The Head of the initiative is Mat Todd and the Head of the Structural Genomics Consortium is Aled Edwards. There is a general email address (chemistry@thesgc.org) but it's best, if you can, to correspond about everything openly. You can ask a question by starting an "Issue" (which is something where you might expect a solution, so that the Issue can be resolved, or "closed") or a "Discussion" (which is more open-ended) - the tabs for these are both above.