Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • electronic lab notebooks

    How do you document your bioinformatics research? When I worked at the lab bench I was meticulous in my record keeping in standard paper lab notebooks. When I started to transition to the 'bit lab' I realized that I was doing a lot of work and none of it was being written down. Then I started a system of taking notes in chronological order in an html file and storing important data files in corresponding folders. Nowadays my group is using RedMine, and we mostly use the wiki feature for keeping records, but the wiki is becoming a horrible mess. I need to develop some standards of what we need to record and how to record it but before I do that I just want to see what other labs are doing. (hopefully not nothing)

  • #2
    Originally posted by mike.t View Post
    How do you document your bioinformatics research? When I worked at the lab bench I was meticulous in my record keeping in standard paper lab notebooks. When I started to transition to the 'bit lab' I realized that I was doing a lot of work and none of it was being written down. Then I started a system of taking notes in chronological order in an html file and storing important data files in corresponding folders. Nowadays my group is using RedMine, and we mostly use the wiki feature for keeping records, but the wiki is becoming a horrible mess. I need to develop some standards of what we need to record and how to record it but before I do that I just want to see what other labs are doing. (hopefully not nothing)
    Hi- That's an interesting issue that I think is often neglected, so to prompt discussion here's my 2p... I provide bioinformatics support to our group so I handle 2-4 different projects at a time. My setup to keep track of what I do is:

    - Redmine: Particularly the "projects" features and the wiki pages. This is to document what and why I do certain analyses, just like a labbook. My lab mates have access to it but I'm essentially the only user.

    - svn: To maintain code and programs I can possibly re-use in the future (although an R script to produce a particular figure or a one-line bash script will probably go in a wiki page rather than here.)

    - Postgresql + Python/Django: To archive samples, libraries, metadata etc. Although it has to be maintained, it is much neater and robust than using Excel spreadsheets or scattered notes on the wiki

    So far I'm quite happy with this setup but I'm keen on hearing other people's opinion...

    Best
    Dario

    Comment


    • #3
      I use http://www.sparklix.com/ which covers my needs well enough (although after a year of using it I'd quite like a better way to check chronology of entries).

      I probably have a 65:35 wet lab:dry lab split, so I'm not sure if for more intense usage it'd stay useful.

      Comment


      • #4
        See: http://www.carlboettiger.info/2012/0...-workflow.html for an interesting use of knitr and git for maintaining a lab notebook. I would like to follow a model like this, but just haven't found the time to set it up. This might be my new weekend project!

        Comment


        • #5
          Originally posted by mike.t View Post
          a system of taking notes in chronological order in an html file and storing important data files in corresponding folders.
          I am doing just that, it works okay, but I do feel there should be a better way.

          There were some good suggestions on this earlier thread:
          Any topic/question that does not fit into the subcategories below. If you're unsure of where to put something, ask in here!
          Last edited by dsenalik; 02-03-2013, 06:15 AM. Reason: Add link

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Best Practices for Single-Cell Sequencing Analysis
            by seqadmin



            While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
            06-06-2024, 07:15 AM
          • seqadmin
            Latest Developments in Precision Medicine
            by seqadmin



            Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

            Somatic Genomics
            “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
            05-24-2024, 01:16 PM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 06-14-2024, 07:24 AM
          0 responses
          12 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 06-13-2024, 08:58 AM
          0 responses
          13 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 06-12-2024, 02:20 PM
          0 responses
          17 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 06-07-2024, 06:58 AM
          0 responses
          184 views
          0 likes
          Last Post seqadmin  
          Working...
          X