OpenWetWare:Feature list/Lab notebook

Status

Significant effort is going to be invested into developing lab notebook features on OWW in the coming months. Your input on this page is greatly appreciated! If you would be interested in participating in the development process or just giving advice, please add your name to the bottom of this page.

Brief description

A good implementation of an online lab notebook for OWW.

Detailed description

Add specific feature proposals here that can be refined and prioritized.

• An OWW lab notebook has lots of features that are useful on their own. In this way, the OWW lab notebook is a goal rather than a feature.
• Every user is most likely to use a core set of features and information organization. May need some specialist "plug-ins".
• BC:Ability to store, query, retrieve structured data would be very useful (e.g. What date did I sequence that plasmid? What freezer box is that strain in etc.) Maybe based on the Exhibit flexible database? See here for an example.
• Provide a page hierarchy for projects (e.g. Thesis->specific aim 1->random experiment 1) and for dates (2007->March->15). The calendar extension provides an adequate solution to the by-date half of this.
• Higher level syntax for inserting common elements into the lab notebook, such as gel images, freezer box maps etc. to remove some of the pain of wikicode.
• A "backup my lab notebook" button might help people be more comfortable using this feature. Would be a dump of just a user's notebook, rather than the entire site.
  • I would enjoy an automatic means for this to happen to a remote site, daily.
• Need to be able to easily search only your lab notebook.
  • It would also probably be helpful to be able to search within a certain timeframe and to search histories of pages.
• Interface to computer peripherals is important.
  • Easy way to add tiff gel images
  • Interface to label printers -- copies of labels go into the notebook. Bar codes.
  • Video recordings of lab bench work (security cameras with motion sensors, audio capture)
• There are commercial products in this space
  • Study commercial products for good ideas and steal them.
  • [1]
  • [2]
  • [3]
  • [4]
  • [5]
• There are other open source projects in this space.
  • [6]
  • [7]
  • [8]
  • [9]
  • [10]
  • [11]
  • [12]
  • [13]
  • [14]
• See these articles on capturing semantic information in the ELN.
  • [15]
  • Polonsky A. et al. (2006) Semantic Laboratory Notebook: Managing Biomedical Research Notes and Experimental Data. Third European Semantic Web Conference (Industry Forum, ESWC 2006), CEUR Workshop Proceedings, Vol. 194.

Issues

1. How does information get organized ... by date, by topic or both?
   • Linking allows you to do both. However, most folks will likely have one mode they prefer to work in so it probably makes sense to offer templates tailored to both types.
2. A robust timestamp and digital signature scheme would be a plus
3. how can we make the lab notebook more useful for collaborating parties (the most typical collaboration might be PI/Grad student).
   • For instance, Cameron showed a timeline tool that would provide some pretty helpful information for a PI that wanted a window into a student's lab notebook.

Previous discussion

Add protocol to my notebook

Could have a click feature on protocol pages that would automatically put a link to the protocol on a sub-page of the userpage like User:Jasonk/Protocols. This could also automatically add the protocol to the user's watchlist.

It would be nice to link to the "permalink" so you easily know what version of the evolving protocol you used. It would seem like this would be good to integrate into a lab notebook feature, so you could say, "I followed this protocol" and have it easily link to current permalink for that protocol.--Skoch3 13:13, 16 July 2007 (EDT)

Interested community members

• Barry Canton
• Jason R. Kelly
• Steve Koch
• Maureen Hoatlin
• Tom Knight
• Cameron Neylon
• Julius B. Lucks
• Alexander Polonsky
• Heather Etchevers