OpenWetWare:Feature list/Lab notebook/2007 Oct Brainstorming

OWW will begin a major effort to implement new technology features that will make using lab notebooks on OWW easier. We had a brainstorming session (teleconference & wiki chat) Friday October 5, 2007 at Noon EDT to collect ideas for these features.

Features List

Steve tried to put the major ideas into the following table. It may be a good idea for everyone to vote on features they'd really like to see (even those that weren't at the meeting!).

Proposed Features & Priority Votes

Feature	People who think this is a priority feature (try not to vote for them all)
A "search within my stuff" button added as part of the skin	SJK
Ability to email to existing or new wiki pages	SJK
Some kind of autosave or other mechanism to make it easy to add incremental bits of data	SJK
Cut an paste to and from the table editor	SJK
A button "create new page from this page (template)"
Barcodes to identify wiki pages (labels)
Automatically prepend user-identifier to file uploads\
Click box on the side for easily inserting tags

Teleconference & Chat, Friday October 5, Noon Eastern Time

How to connect to the meeting Call this phone number: 617-452-2163 Get the wiki chat going: Click on the "chat" button at the top of any page, and then go to the "lounge." As of 11:50 EDT, chat isn't working for Steve

Since we have settled on a date and time (Friday, October 5, Noon Eastern Time), I have archived the scheduling grid.

The meeting will be a teleconference and chat, as is done with the OWW Steering Committee monthly meetings. We will post the phone number and chat link in this area, once we've worked out those details. Hopefully we have that info out soon, but as a last resort, visit this page a few minutes before noon EDT on Friday to see the up to date links.

Proposed meeting agenda

A few common themes from peeps' pre-meeting thoughts

Abiilty to easily insert images and files into electronic lab notebook Specifically: gel images Similarly: automatically streaming data to OWW database.

Better search and tagging

Ability to add a lot of short notes and / or data throughout the day w/o saving or logging in each time

For foreseeable future, data processing will necessarily be off-line (e.g. Matlab, LabVIEW)

Templates for starting off lab notebook entries

1. Chaos of getting chat and telecon working
2. Introductions
3. Implementation Discussion
4. Feature Discussion
5. How to move ahead

Julius B. Lucks 21:07, 4 October 2007 (EDT): I added an implementation discussion before the feature discussion because I think the former is more fundamental to what we are trying to achieve. To me there are two main implementation routes

1. Implement everything as server-side by adding wiki-extensions, etc. The main feature of this is that users primarily interact with the service through their web browser.
2. Implementing a set of tools as an API for consumption by client-side programs. For example, most of the common blog platforms (Wordpress, Blogger, etc.) have XMLRPC API's that allow client-side programs to fetch and post content on the blogs.

The former approach has the advantage of being controlled by OWW with an OWW look and feel. However, it is also very complicated to integrate a lot of the features into the core wiki smoothly (graphs, spreadsheets, etc.) The latter approach has the advantage in that users can continue to use the graphics programs and spreadsheets that they already use. The minimal API just offers an avenue for posting and retrieving content from the wiki. The disadvantage of the latter approach is that client-side software has to be developed to use these api's. However, there are popular tools that already exist that can interact with such API's, and this list is growing (especially due to the popularity of Google's GDATA API's). See my notes for more information.

Pre-meeting activities

1. Electronic Lab Notebooks (ELN) elsewhere. As Tom Knight pointed out on the parent page, there are a lot of non-OWW people working towards these same goals. I spent some time looking at his links and it would probably be useful for others to do as well. Here are two that were fruitful for me:
   • UsefulChem very active use of wiki-style ELNs.
     • Are there any UsefulChem people who are also OWW members and would attend the brainstorming session? Sure - I'll be there! (JC Bradley)
   • Oak Ridge ELN and specifically, this page lists a lot of features they've added over the years.
   • ChemSpider is going to be Wiki-enabled in the future. We have allowed structure deposition so far. Wiki-enabling for curation of the chemical structures is coming. Ultimately My ChemSpider will enable "notebooking" for chemists
   • Southampton Blog Book - have a look at the 'bioblogs', we are trying to find the best way to organise the metadata and also have some cool features built in such as label printing (which you can see - but it will print to a printer in Southampton) and template posts (which you can't see without edit permissions)
2. If you have time, add your picture and create a sub-page with your own personal pre-meeting thoughts (as disorganized as you like). You can see "Steve Koch" for an example of how to do this.
3. Add proposed agenda items and please edit this page with any improvements you can think of!
4. Take a look at the previous suggestions for lab notebook improvements on OWW.

Meeting Notes

Jason R. Kelly: Sorry this is a mess, but most of the stuff mentioned should be in here, feel free to add/edit anything i missed.

• Introductions
  • Steve Koch & Diego Ramallo - UNM
  • JC BRadley
    • wikispaces – they use for their notebook.
    • blog is for recording milestones and things that happen, link back to exp
    • they want to trace back to the raw data.
  • Julius (cornell)
    • arxiv.org
    • used a private wiki for lab notebooks, use public wiki in the future.

Implementation of client-side

Advantages:

• easier to implement stuff like drag and drop, etc.

Dis*advantages:

• requires client*side developing

Austin: Decide what it is we want before figuring out the implementation

What do the users want? Steve: Students on private wiki / students in physics Concerns:

• uploading images is a headache
• People want to put in a bunch of numbers over the course a few hours and they don’t want to have to save the page over and over.
  • entering data without having to do annoying things like logging in or save

• love the table editor.
  • wiki spreadsheets – would be difficult to implement
  • ’’’cut and paste from wiki table to excel (seems like a concrete thing) ; might be something in xhibit that lets you connect to google.’’’
    • Austin worried about keeping data in google.
    • Bill says that it would be more for export and import
    • Barry Data on the wiki easy to move matlab or excel, would be good to store on the wiki in a low tech a means as possible.
  • Bradley: sharing the way you do the analysis might be reason

• TOM: would like to see an easy interface to medium of paper. Would be nice to easily put a scrap of paper into the notebook.
  • someone sends you a plasmid map in the mail, oligo order comes with paper you want to include, protocols come in paper form as well.
  • this is the subset of the image input process.

• • Steve: scan to PDF tool is useful, then would be able to post directly to OWW. Many of the pdf machines have methods to email automatically. If you could email to your lab notebook page that would be great.
    • Steve: social text every page gets an email address, so that you could email to contribute.

• Barry: Be able to get the images linked from alab notebook page of a particular date automatically. If I save my gel image with a particular date format in the name, it would be automatically linked from that day’s page.

• Jason: would like to have barry’s idea extended to everything I do on the wiki. Would like to know everything I edited and everything I uploaded on a given day, and easy way to browse through that stuff. Basically a better UI for browsing these thing.

• Tom: track labels that he prints. When he finds a tube with his initials and his date he needs to go back to his lab notebook to figure out what the heck it is.
  • unique ID could work

• Cameron:

Labels: We have a single post per item and systems that will auto*generate a label based on the post id also instruments that blog so the dates are taken care of * but several of these kind of things have been worked out in our system * how easy to transfer to a wiki framework I don't know but not many of them survive *80 :)

• Jason: would like to have the organization created automatically
  • e.g. Barry has a pretty nice system for automatically organizing things by date and project, we need to make it so this can be implemented in a turn-key way.

Austin:

• • Austin keeps his stuff private so that he can have his stuff sepreate from other peoples stuff
  • Is there an easier technical solution to keep things separate
    • Bill: Look at namespaces
    • Austin: should we have sub-wikis for each lab notebook?
  • Would it be possible to keep the files separated for each person
  • Steve was suggesting that if you upload a file I should be able to specify its filename, but it should almost by default be BarryCanton/foo.pdf
  • sub*wikis

Search:

• • you could just search your lab notebook by having a namespace
  • search “every page that I’ve edited” or every page in the barry canton namespace
    • ‘’’every edit would probably be sufficient, and would be extremely useful independent of lab notebook’’’

• • • Bill: Look at namespaces

Tagging:

Steve – tagging on the private wiki using categories.

• • might be nice to have a tag box
  • how are they specifically using it?
    • write down ideas in random places and add category steveResearchIdea
  • would be easy to use them
  • Bill: Austin has good example of "dynamic page lists" which may be what Steve needs

Barry:

• uses date tagging heavily
• sounds like the most useful “tags” for lab notebook would just be ‘project’ and ‘date’
• dynamicPageList might also allow for tagging as a form of organization.
  • doesn’t seem like
• Barry: different point about tagging.
  • barry finds the notebook useful for planning what he’s going to do. Feature that keeps track of what are my next actions in 4 different projects.
  • Bill: there exist fairly nice todo list extensions / steve needs a todo list badly

Adding little bits of data as you go along

• making it easier.
• Austin thinks this is a big problem, keeps everything in an editor and copies it over to the wiki at the end of the day.
  • Bill: lot of individual difference in the way to browser and mediaiwki interact and it causes problems in the lab.
  • is there a way to connect to the DB directly, rather than through the browser.

Wiki Lab Notebook Brainstormers

• 

  Steve Koch
  Steve's pre-meeting thoughts

• 

  Julius Lucks
  Julius's pre-meeting thoughts

• 

  Austin Che
  

• 

  Jason R. Kelly
  Jason's pre-meeting thoughts

• 

  Barry Canton - Thoughts
  

• 

  Diego Ramallo
  

• 

  Tom Knight
  

• 

  Maureen Hoatlin
  

• 

  Bill Flanagan
  

• 

  Jean-Claude Bradley
  

• 

  Antony Williams ChemSpiderMan
  

• 

  Cameron Neylon
  Cameron's pre-meeting thoughts

• 

  Ricardo Vidal
  Ricardo's pre-meeting thoughts

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15 April 2024

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					18:48 Nkokkula talk contribs uploaded File:MarginationSize.jpeg ‎(Reprinted with permission from Namdee, K.; Thompson, A. J.; Charoenphol, P.; Eniola-Adefeso, O. Margination Propensity of Vascular-Targeted Spheres from Blood Flow in a Microfluidic Model of Human Microvessels. Langmuir 2013, 29 (8), 2530–2535. https://doi.org/10.1021/la304746p. Copyright 2013 American Chemical Society.)
					18:34 Nmhatre talk contribs uploaded File:NonlinearGradientDevice VaryingHorizontalChannelWidth.jpg ‎(Device made by Abe et al. which creates a nonlinear gradient by varying the horizonatal channel widths. "Reprinted with permission from Abe, Y., Kamiya, K., Osaki, T., Sasaki, H., Kawano, R., Mikia, N., Takeuchi, S. Nonlinear concentration gradients regulated by the width of channels for observation of half maximal inhibitory concentration (IC50) of transporter protein. Royal Society of Chemistry. 2015,140. DOI: https://doi.org/10.1039/C4AN02201G. Copyright 2015Royal Society of Chemistry.")
					18:17 Nmhatre talk contribs uploaded File:NonlinearGradientDevice.jpg ‎(A nonlinear gradient device created Selemovic et al. "Reprinted with permission from Šeila Selimović, Woo Young Sim, Sang Bok Kim, Yun Ho Jang, Won Gu Lee, Masoud Khabiry, Hojae Bae, Sachin Jambovane, Jong Wook Hong, and Ali Khademhosseini Analytical Chemistry 2011 83 (6), 2020-2028 DOI: 10.1021/ac2001737 . Copyright 2011 American Chemical Society.")
					18:12 Nmhatre talk contribs uploaded File:NonlinearGradientDevice.webp ‎(A nonlinear gradient device created Selemovic et al. "Reprinted with permission from Šeila Selimović, Woo Young Sim, Sang Bok Kim, Yun Ho Jang, Won Gu Lee, Masoud Khabiry, Hojae Bae, Sachin Jambovane, Jong Wook Hong, and Ali Khademhosseini Analytical Chemistry 2011 83 (6), 2020-2028 DOI: 10.1021/ac2001737 . Copyright 2011 American Chemical Society.")