OpenWetWare:Feature list/Lab notebook/2007 Oct Brainstorming/Norville

Last August I had some ideas for a Google lab notebook that I sent to them.

Here are the ideas, in case some are helpful for this project (I haven't heard back from anyone who wants to make it there yet.)

Note: this probably applies primarily to researchers in the biological and chemical sciences. Other researchers (such as experimental physicists) probably have different requirements.) I haven't talked to people outside my area to see what they need.

Protocols: the Bread and Butter of the Scientific Effort

First take a look at a protocol at openwetware.org--an example is the ligation reaction: http://openwetware.org/wiki/DNA_ligation

These general protocols (for molecular biology) are just moving online now (and it is really helpful!) In the past you would have to spend hours in the library looking for them or ask a friend for them.

An online lab notebook could ease the scientific process by making it easy to store personal protocols and protocols in development in an intelligent way.

One fundamental difference between people who keep scientific notebooks and people using applications suites in general (like Google Docs or Microsoft Office) is that scientists tend to use protocols again and again (especially in biology.) Once I have a working protocol I tend to copy it (with a copier) and paste it into my lab notebook every time I use it. (The problem with doing this is that I need to search for protocols when I need them--some people keep a separate file for them, others just look back through the notebook to the last best instance.) There are protocols that people create using scientific papers as a guideline, there are protocols for company products (for example qiagen miniprep handbook which is attached), and there are published protocols available in books or journals (such as Nature Methods.) Helpful to you is that more and more people are searching for protocols online (openwetware.org is an MIT effort for posting protocols online) these days rather than looking them up in books.

features that would be helpful for protocol use in a notebook application suite:

-a separate protocol storage section, -a way to share working protocols with the community (see openwetware.org) -nice ways to paste protocols into a general, sequential notebook on demand and easily modify them with optimizations -a way to mark protocols as working or not working -have a separate notebook document and mark on the same page in the notebook what happened in the specific real instance of the protocol being followed on a specific date (as compared to the ideal protocol that is used again and again)

- Data: Images and Tables Images and other data figures are of key importance to the scientific effort. People currently paste a copy in their notebook and save the digital copy somewhere. If you want a digital copy then sometimes it is easy and sometimes it is hard. From some software and programs the best you can do is printscreen. So having a way to modify printscreens easily might be useful. In the past when I have considered creating a notebook stored on my computer the biggest roadblock was nicely porting the images into it. Images tend to be used again and again. It needs to be easy to put them in the notebook and write around them, and possibly add a label to them. On the other hand, perhaps automatically storing them in another place where they can be searched, go into documents and other presentations is also useful (picasa is a good start.) Some people might like to create tables or "sketch" a figure in the book. - Dating Pages and Search Dating a notebook is important. The date on which research occurred is useful for patent applications, and also help a researcher search back through the notebook sequentially if they forgot when they certain experiment (although such things may become unnecessary in the presence of good search capabilities.) Once a notebook becomes a certain size you might want to port it offline as notebook number x. Of course with google's search capabilities you can also search through the notebook by other factors as desired. - Data Sharing Sharing data from the notebooks is also important. As I mentioned previously, people are finding more and more of their protocols online. People may want to post them publicly for sharing once they have a working protocol. People also may want to share protocols within their lab or the notebook itself, even after they leave there.

Currently students are in many cases "expected" to leave the lab notebook book behind when they leave the lab (the book At the Bench by Kathy Barker describes the expectation for this.) There are reasonable motives behind this (accounting for grants, principle investigators wanting to keep information in the lab after the student leaves.) However, to the people who create such an intimate document, that documents their learning over such a long period and stores their working knowledge, leaving behind the notebook seems unfair. Leaving behind an electronic copy or a protocol list, or a locked electronic copy that can be opened in the case of a grant review, and being able to keep one in addition seems more fair. So people may want to share a copy of the notebook itself or selected sections within it (probably internally within a labgroup.)

Scientists also tend to create reports about the data that they can show to their professors or manager. This could be a picture with some text. Having a place you can store such a report online is quite useful for several reasons. 1. Currently many professors/supervisors have a blackberry and don't want you to send large files. 2. Even if you send the files it may be hard to view them appropriately. 3. If the reports are stored in a viewable location online, the professors/supervisors can view them easily, comment them, and review them later as appropriate. Scientists also probably want an option to easily backup their work. They might want to burn it to DVD or save it to their computer--so an easy way to create backups or a reminder system for this might be nice. Security may be a big issue for online notebooks. If the notebooks get hacked it will be very troubling for the scientists involved. It might be good to lock entries after a 2 day window, so that the notebook is hard to destroy. - Useful Ads Scientists always want to keep up to date with the newest information and the latest protocols and kits. Currently the leading edge of knowledge tends to diffuse from lab to lab. Since you will "know" what someone is working on by searching their notebook like you do for gmail, you can be a resource for newer products or help guides for the procedures they are using or chatgroups of scholars using similar protocols. Scientists may be very interested in the information contained in appropriate ads and the appropriate companies may be very interested in providing it.

A Nice Link to Google Scholar Bringing up papers that are relevant to the protocols the researcher is currently using is very valuable. It would be cool if you could copy the Goolgle Scholar link and then it got transformed into a citation when it is placed in your notebook (a sort of magical Endnote software utility.) Some biologists in the CSAIL lab at MIT are enamoured with the features of Papers 1.0 (see http://mekentosj.com/).