Open shntnu opened 4 years ago
in broadinstitute/hepatocyte_cellpainting_sigma#25 @shntnu writes:
issues to discuss the experiment, and PRs to describe the implementation
Based on this approach, you would create an issue related to this experiment and describe your results in the issue and seek feedback via the issue, not the PR
I have copied below a set of our (past) ELN requirements. These have evolved ever since, but still are more or less representative.
Priority | Feature | Minimal requirements |
---|---|---|
High | Tagging | Anyone can create tags, no constraint on no. of tags |
High | WYSIWYG | Drag drop images |
High | Searching | Searchable using tags, save searches, boolean operators |
High | Backup | Should be able to backup using Crashplan or Broad servers |
High | Export | Should be able to export notes in a common format |
High | Linking | Should be able to link to other notes |
High | Inline comments | Comments should not be editable by others, but others should be able to "resolve" or reply to it. Comment should automatically be associated with author. |
High | Large amounts of content | Each note needs to be able to handle an appropriate amount of images/data |
Medium | Collaborative editing | No conflicts if multiple people edit |
Medium | Modularity | Each note should be a separate entity |
Medium | Notification | Be notified if you are tagged, or a page is updated |
Medium | Task management | Assign tasks to yourself or others |
Medium | Access to outsiders | When we occasionally want to share a result with someone not regularly using the system, we want to send them a link they can access via web browser |
Low | Offline access/editing | This would be convenient |
Low | Revision history (esp in case of accidents) | Be able to view changes to notes |
Low | Smooth transition to writing papers | Be able to construct a paper outline based on notes |
Really low | Permissions/security | We probably don't care about this feature; nearly all content would be available to all |
When creating a note (=issue), give the title some thought. Here's what we've followed:
Here's a great template for lab notebooks on GitHub https://github.com/uwescience/shablona
00.<name>
, 01.<name>
, ... 00.<name>
, 01.<name>
, ... input
, output
, and figures
x.generate-figures.ipynb
in each folder
I just have a few comments on this, though I am aware that it is a complex challenge:
The folder structure doesn't cover multiple iterations of a given analysis. I will exemplify this with a use-case: Let us say I perform an analysis and, after discussion, we conclude that we should try changing some parameters and see if it improves. We then need to compare these different results. My proposed solution to this is to have (optional) datetimes for every time an analysis was run.
I still have to digest some of the ideas and challenges, so I may come back to this issue down the line.
I just have a few comments on this, though I am aware that it is a complex challenge:
Thanks for sharing your thoughts @afermg! I've updated my comment
@afermg I've now created https://github.com/broadinstitute/carpenter-singh-lab-standards/blob/main/01-lab-notebook.md so let's continue the discussion in that repo
Here, we define the elements of an effective lab notebook.