Wednesday, March 09, 2016

University of Toronto post-doc shares lab notes

The University of Toronto publicity department is making a big deal of Rachel Harding. She's a post-doc in the Structural Genomics Consortium (SGC). She works on Huntington's disease.

Here's the link to the press release and the first few paragraphs [Researcher is an Open Book: First to Share Lab Notes in Real Time].

Faculty of Medicine researcher Rachel Harding will be the first known biomedical researcher to welcome the world to review her lab notes in real time. The post-doctoral fellow with U of T’s Structural Genomics Consortium (SGC) is also explaining her findings to the general public through her blog. She hopes her open approach will accelerate research into Huntington’s disease.

“This should drive the process faster than working alone,” Harding says. “By sharing my notes, I hope that other scientists will critique my work, collaborate and share data in the early stages of research.” Her research at SGC is funded by CHDI Foundation, a non-profit drug-development organization exclusively dedicated to Huntington’s disease. Both organizations aim to accelerate research by making it open and collaborative.

Her approach is intended to leverage the experience of a community of scientists. Individual researchers often still work in relative isolation and then publish only their positive discoveries, usually years after the experiments were actually done. Thus, scientists often pursue similar ideas in parallel and miss many opportunities to learn from each other’s mistakes.

She has started by publishing raw data and play-by-play details of her first effort on the CERN open digital repository Zenodo. She also posts regular updates on her blog Lab Scribbles, where she includes an experimental summary written in lay terms.

It's been over 35 years since I first starting thinking and talking about electronic (computerized) lab notes1 and it's been over twenty years since I first heard discussions about putting them online. I seriously doubt that Rachel Harding is the first biomedical researcher to put lab notes on the web. I'm also very skeptical about her keeping up the practice for very long.

Not only is it boring and tedious to write your lab notes in a word processing program but it's kinda embarrassing to post everything you do in the lab. At least it would have been for me. I made lots of mistakes and there are lots of R-rated words and phrases in my notes.

Let's keep an eye on this experiments to see how it goes. So far there are four items on the Zenodo website. The first is a Word document containing a few brief notes from Jan. 6, 7, 9, 11 and 25. There are brief notes posted on Feb. 6 and two on Feb. 11. I hope this isn't the extent of her lab notes.

The blog is Lab Scribbles. There are a few posts. It's interesting but I'm not sure anyone is going to read it even if you're interested in Huntington's.

Has anyone else experimented with open lab notes?


1. I still have a few floppy disks with those attempts from about 1981. Unfortunately, I don't have a machine that can read them.

21 comments :

  1. I also strongly doubt that she is the first. And yes, I understand the posible embarrassments of open lab notes. But I think you are just showing your age with the "boring and tedious to write your lab notes in a word processing program" quip. I'm hardly a spring chicken being 45, and even I find writing anything by hand far more tedious than typing, and I think the younger generation likes writing by hand even less.

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  2. Two comments:

    1. If one were to pursue open lab notes, I would advise careful selection of tools. One possibility is an app like LectureNotes (Android) - use a tablet with a stylus; write notes longhand with the stylus, importing data and graphs as PDFs and JPGs; automate a daily export / upload to a file sharing service like Dropbox or Google Drive.

    2. Comment #1 notwithstanding, I think open lab notes are a terrible idea. You can forget all about IP. But even worse, it'll just give rumour-mongers and other duplicitous individuals with ulterior motives lots of ammunition to drag good science and good scientists into the quagmire of gossip and social media irrationality.

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    1. now that second point is no doubt true, especially by those who a) have a vendetta against science and b) have no idea of how difficult and challenging it actually is on a daily basis.

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  3. Larry asks: Has anyone else experimented with open lab notes?

    In a way yes. My experiments and ideas that led to new models are always open access, in science related forums. I this way seek out informal review.

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    1. But of course one drawback with public forums are the nutcases (like Diogenes) who like to derail discussions.

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    2. Yeah, Diogenes is the nutcase. That's it.

      -jaxkayaker

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    3. Having religious reasons against a scientific theory is worse than religious reasons for it because at least in the latter case the person is not intentionally trying to stop its progress.

      Are you thinking of any particular examples here, Gary?

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    4. I had hundreds of pages of examples on my mind. Things are though better than they were. Progress is here measured by how fewer times I get spit on, by those who are supposed to know better.

      Anyway, now that I linked to one of my favorites, in that forum my cognitive science related notes and activities are available by looking at Topics Started:

      http://www.kurzweilai.net/forums/profile/gary-s-gaulin

      This has been a convenient way of finding information that I needed again.

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    5. Sorry, Gary, if I was unclear. I meant examples of worthwhile scientific ideas that are rejected because of religious preconceptions. Your useless crap doesn't qualify.

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  4. To convert my old lab notes to Word would take a long time...and I dont even know how I'd created some of the figures....
    or I could just take a clear picture of them with my cell phone and upload that. That would take all of a few minutes!

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  5. All of my lab notes are already on Word. If anyone can find me a 5 1/4 inch floppy drive, I am willing to share them all.

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  6. Why sure. I've been working on solving the molecular structure of protein X for 10 years. And so have my competitors who have been trying to scoop me for years. And we've spent upward of a million dollars in grant money trying to solve the crystal structure of protein X first. And my competitors know I'm trying to solve it too.

    And only the person who publishes first gets any credit at all. And if you don't publish first, your tenure will get denied.

    Here, competitors in all countries. Come look at my electron density map as I trace the backbone. Sure.

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  7. https://en.wikipedia.org/wiki/Jean-Claude_Bradley

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  8. I sometimes report my more painful mistakes on facebook, and yeah my lab journal is full of self-deprecating expletives too xD

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    1. Worst mistake ever in terms of frustration was 2 weeks of cell-culture lost to late evening lazyness and lack of focus. I can't believe how many idiotic mistakes I made. Next day's Journal entry says "please kill me now". That will never repeat itself!

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    2. Two weeks? Lite-weight! ;-)

      I lost several months early in my PhD when my numbskull thought it would be clever to knock-out protein expression from individual genes in a polycistronic operon by introducing stop codons into each gene by turns. At that time, I didn't know what had been demonstrated decades earlier - that premature termination of translation in bacteria usually leads to premature termination of transcription as well (and thus no downstream gene expression from within the operon). Well, that was the stupid and hard way to learn about the promiscuous activity of Rho protein.

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