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Life in the Drug Labs

Write It Down, Write it Down

A couple of years ago, I wrote about electronic lab notebooks, and pointed out how much better they’ve made my record-keeping. My new job also uses an electronic platform, to my relief, and if anything it’s better implemented than the one I was using before. It’s clear to me, that software lab notebooks are the only way to go. Drawing the structures, setting up duplicate or related experiments, attaching all the data files from LC/MS and NMR, the ease of retrieval for patent filing purposes, the ability to search structures across a whole organization’s experience – there’s no substitute. (One thing they don’t handle well, though is TLC data, which I was just talking about – anyone have a solution for that?) But that aside, going back to paper would be agonizing; a directive to use hardbound notebooks would induce terror and dismay.
Still, both of the electronic notebooks I’ve used are in-house jobs. I’ve had some mail wondering if I have any recommendations among the commercially available software, and that’s a question I can’t help out with at all. So I thought I’d throw this one out to the readership: what’s worked for you? And how much did it cost? Is there anything open-source that’ll do the job? (I’ve heard of Wetlab and OS-ELN, but know nothing more about them).
And here’s another question, which is more of a poll. Are you using paper or pixels for your notebook? If you answer in the comments, which I’m glad to report seem to be working again, mention what kind of work you do and if it’s in an academic or industrial setting. I’m curious to see if the expected correlations show up. . .

37 comments on “Write It Down, Write it Down”

  1. Derek says:

    IDBS (UK) that sell ActivityBase also has a ELN product that we are about to pilot here at UofMN. Maybe be able to update you in afew months

  2. Reg says:

    I started a new job about six months ago (industrial research), and the new company just started using e-notebooks. I think it’s some combination of commercial software and in-house modifications. TLC isn’t a problem – one option in our system is to add a TLC plate, which appears on screen and can be “spotted” using the mouse. Very easy.
    The biggest negatives are probably things that will be fixed as computers improve. It’s difficult to flip from one experiment to another, if you want to quickly compare conditions or check data, for example. Changing from one “page” to the next is glacially slow, and it’s very hard to quickly jump back and forth between experiments without tearing your hair out in frustration. (As at many companies, our software is “networked” which means “slow”, especially at busy times of the day.) The other issue is that our system is currently desktop only – no computers in the labs. Which means you make notes on scraps of paper and then transfer them when you’re at your desk. That will change (with more $$$ for laptops), but it’s still an issue if your lab space is limited – where do you put the laptop (and it’s attendant cables and power cords) and how do you protect an expensive laptop from spills and contamination. It was much easier to keep a paper notebook at your bench, and stash it away in a drawer when it wasn’t needed.

  3. Walt says:

    Derek, As for the TLC data, I used to just photograph it and attach the file — usually it is qualitative. If it is quantitative, scan and attach it.
    Concerning the poll, I am a biochemist for 28 years in pharma and now a consultant at a law firm. Unfortunately the law business is lower tech than I expected — not good use of pixels. Less than 50% digital. The patent (and pharma) business desperately needs software to systematically handle Markush claims.

  4. Anonymous says:

    I just scan my TLC plates on a scanner, save it as a pdf and link it to my notebook page.

  5. Throwback says:

    I am currently in a post-doc position where everyone accept myself uses hardcover notebooks. I use a crude excel spreadsheet I put together as soon as I bought a laptop halfway through my graduate work. When I asked my new adviser if I could keep my notebook electronically, he was quite hesitant but conceded. It allows me to paste my reaction from chemdraw and have all the calculations done for me (so as to minimize mishaps). The best thing, is the ability to copy and paste experiments and then easily modify them (huge time saver). Unfortunately, if I miss a simple change (like the MW of the product or where I bought a reagent) it will be confusing to people in the future. This very crude system, however, has to be less confusing than my old lab notebooks from grad school!

  6. George D. McCallion says:

    Derek, my recent position was within Pharma. (laid-off due to ‘redundancy’). Anyways, the Group that I was with went to all eLNB. It was a semi-smooth transition, but I have some reservations on eLNB in general.
    First, your TLC question is valid. There IS a solution: if You have a scanner IN THE LAB (NOT IN THE HALLWAYS, where everyone can get exposed to silica gel…silicosis) place a strip of (clear) packing tape across the plate (post visualization, of course). Scanning will provide a VALID analytical result.
    And furthermore, this technique is cGMP valid! YES IT IS!!
    As far as notebooks go, I feel that they can weed-out those who like to hide in their (notebook) pages and simply say, ‘it’s been done’; now it must be documented.
    Tie this in with one’s performance, and You can easily tell those that DO science versus those that they SAY they are scientists.
    It also lends itself to reading into how a person follows proper documentation (there are SOP’s for this) of an experiment.
    My 2 bits….cheers!

  7. BIotech Brit SD says:

    I work at a mid size Biotech in San Diego and we’ve run the Cambridgesoft (CS) ELN for a few years. The CS product can utilise the TLC drawing tool in Chemdraw, which works for straightforward TLC plates, but gets a bit cumbersome for more detailed plates (small spots, arch shaped spots, varying degrees of faintness). For simple plates however its just as easy to just report Rfs. You could always take a photo or scan and attach that.
    Thinking back to my PhD, people used to staple in the original aluminium backed plates into their labbooks. Not sure how much info they would be able to see after a year, but opening their books always released a nice cloud of silica dust, yummy.
    We use paper to store, but if patent law changes (to first to file) we’ll go to pixels. So much easier for the user and for admin.
    In our experience CS and Symmx are the two main products, each is probably equally good with its own nice features and issues. A true comparison is difficult as they are always moving targets. CS seems to be becoming more the industry standard.
    BTW, I am a Medchemist, but have been involved in ELN admin.

  8. anon says:

    I know this question is terribly dull but while your’re at recommending electronic note books, can anyone recommend any timesheet software. I just wanted to save myself the trouble of knocking up an excel spreadsheet … anyone?

  9. Nick C. says:

    I do optical materials development at a US DoD lab, and everyone I’ve worked with here uses a paper notebook. Up until recently, my wife also worked as a chemist doing materials chemistry at a university-affiliated contract lab, and no one there used anything but paper, either.
    I’ve never even seen an electronic lab notebook, and that fact makes me, at 33 years old, feel like a dinosaur. I’ve thought seriously about buing an ASUS eee or some other subnotebook PC and using conventional software (Open Office or the like) to keep my notes, but I’m not sure that such a system would offer me enough advantages to make it worth my time.

  10. Rich Apodaca says:

    Derek, I’m curious about the hardware you used in both cases. A lab notebook needs to be tolerant of some very demanding conditions – solvent spills, chemical contamination on the keyboard, and dropping to name a few.
    Then there’s the issue of ergonomics – a laptop computer has a screen that might not be visible at certain angles and a keyboard that needs to be used often while standing or in some other awkward position.
    Tablet PCs seem nice, but still pricey.
    These are all things a paper notebook handle in stride. What about ELN hardware?

  11. ZAL says:

    I’m a postdoc in an academic lab, doing organic synthesis / organometallic chemistry. I use and always used a paper notebook, also during my time as grad student. In academia there seems to be no urgency to change to the electronic system: maybe that’s because most often it has to be an “in-house” job, as Derek pointed out, and around here there are not many people with time/will/capacity to do such a job without being paid for it.

  12. Trevor Covert says:

    I’m in an academic genetics lab, it is all paper, and I have not seen nor heard of any other labs on campus using electronic notebooks. We do a lot of supplementary data repositories in Excel and other programs.

  13. Biotech Brit SD says:

    Rich,
    AZ have (TMK) a system where they clone their desktop PCs to flat screen monitors by their hoods, they then only need a monitor, keyboard, mouse, and they can all be on a pull down lever platform which stays out of the way when not in use.
    Wireless networks make life easier, but not everyone (inc us) have them.
    I’ve heard of another company (don’t remember who) who have a recharging stack of laptops by the entrance, when the scientist walks in they grab one and take it to their bench. I can’t remember if they had ethernet conns at their bench, a wireless network, or used an offline feature.
    We just hijack any communal PCs in the lab (label printers, HPLCs) to run the client, plus get as many stand alone PCs we can. In Medchem there is a limit to how much time you need to spend recording data real-time. More GLP environments however are different.

  14. Ken says:

    I’m in an academic lab at Virginia Tech. The lab only started a year ago so we hit the ground running with Cambridgesoft’s Enotebook. It’s terrific. Somewhat of a pain to get implemented properly as they prefer you pay 10 grand to get an install team. Didn’t seem practical for our group of 10….
    In any case, it’s really taking off. It’s inspired the department to buy a site license so that a few other groups can implement it.
    It’s extremely useful for day to day use. But when it comes to presenting in group meetings, writing papers, presentations, etc… that’s where it really shines…
    And our boss LOVES the fact that he can look into our lab notebooks from his desk at any time. Good way to monitor progress, make sure your grad students are keeping up there lab books propers, and of course to permanently implement your foot up their ass…. 🙂

  15. Biotech Brit SD says:

    Rich,
    AZ have (TMK) a system where they clone their desktop PCs to flat screen monitors by their hoods, they then only need a monitor, keyboard, mouse, and they can all be on a pull down lever platform which stays out of the way when not in use.
    Wireless networks make life easier, but not everyone (inc us) have them.
    I’ve heard of another company (don’t remember who) who have a recharging stack of laptops by the entrance, when the scientist walks in they grab one and take it to their bench. I can’t remember if they had ethernet conns at their bench, a wireless network, or used an offline feature.
    We just hijack any communal PCs in the lab (label printers, HPLCs) to run the client, plus get as many stand alone PCs we can. In Medchem there is a limit to how much time you need to spend recording data real-time. More GLP environments however are different.

  16. Stone Age says:

    I am a postdoc in academia, and of course working with paper, instead of pixels. For some tasks, I am using Excel, but not as a notebook.
    I have 2 questions in this context:
    1) Why do we still waste billions of hours of our very limited time typing spectral data on paper (in academia). In my eyes this is a real waste of time.
    Electronic spectra (submitted in a standardized format) on the other hand would offer lots of useful features, such as the direct search for compounds according to their spectral properties – not just within limited databeses, but throughout the complete literature…
    2)My favorite operating system is Linux. The ONLY reason why I am still forced to work with Windows when doing chemistry is the fact that very useful software like Chemdraw is not produced for Linux. Is it so difficult to offer a precompiled version for a limited set of most popular Linux distributions? Probably poor philantropic Bill Gates would loose a few $ under this scenario…

  17. industry guy says:

    Working for a German company in the US, we use German developed software which I have to say is pretty good. Links to spectra, searchable across all of company sites, and interface actually nice and easy to use. Company is at
    http://www.enso-software.com/WebSite2005/Default.aspx
    Not quite like the wonder drug factory’s CLJ though Derek, but still quite nice:)

  18. Chrispy says:

    I have always believed that there should be no “intermediate” scraps of paper between the bench and the notebook. All notes, observations, etc. should be written into the lab notebook. Be very suspicious of people with very neat lab notebooks! Often the data is missing or wrong.

  19. burt says:

    “Chemdraw is not produced for Linux”
    Have any of the open-sourced Chemdraw knockoffs progressed?
    Have you tried OS X? It is way better that Windows, particularly when running graphics software like Chemdraw. I’d argue OS X is also better than LINUX.

  20. Stone Age says:

    burt,
    OS X may be nice, but as there is luckyly not just Microsoft producing an operating system, the same is true for hardware…
    By the way: I do not want Chemdraw for free. If a company has a good product, there are always people going to pay for it, even those using Linux…
    Linux is not command line based hacker software any more. Graphically there is no big difference compared with OS X. But there is an increasingly big difference in speed compared with memory inefficient Windows…

  21. Lou says:

    I’ve lived in the ivory tower made of paper.
    I think the only reason why academia sticks to paper is money and inertia. I can’t see an University paying money to implement something like that. They’d have to get money off the grant funders. As for Institutes, that may be different…

  22. Bacon says:

    Is Symyx’s eLNB reasonably cost effective for an academic group? I’d like to get my group going with electronic notebooks from Day-1, however, have concerns about the cost.
    From a report above, CS wants a $10k setup fee? That added to the hardware needed and software costs is probably out of a reasonable-for-academia range.

  23. startup says:

    I’ve been dreaming about going electronic for a long time. CS product turned out to be incredibly hardware-intensive and ill-suited for standalone use. I was excited to hear about the open source ELN’s, yet WetLab is seemingly unable to paste chemdraws, and installation of OS-ELN… well, it overwhelmed me. I guess it is still paper for me.

  24. Frustrated Commentator says:

    I also save TLCs by scanning. A good scanner is only $100-150. I have one in the lab. It allows me to save all the shapes and colors I would be too lazy to put in my little TLC plate drawing.
    I don’t yet have enotebooks, but I have erecords. I decided a couple of years ago not to keep a paper notebook. (We have had fires and many lost notebooks over the years.) I keep synthetic records as .docs (with structures embedded). MS, TLC, NMR, UV, misc. assays are kept as .pdfs. All of the records for a particular lot go into a lot folder. A big disadvantage to this system is the inability to search structures and substructures. A big advantage is the ability to search text with an indexing tool like Copernicus.
    BTW:
    Comment Submission Error
    Your comment submission failed for the following reasons:
    Too many comments have been submitted from you in a short period of time. Please try again in a short while.
    WTF? Corante thinks that all the previous comments to this post were from me and won’t allow me another???
    How hard is this, really? It’s all 1s and 0s.

  25. qetzal says:

    I’ve worked for or with 6 different small to medium biotechs over the past 20 years. None was ever more than ~ 200 employees, usually well under 100. Every one was strictly paper for notebooks. The ones that did GMP used paper as well (for batch records, test records, etc.).
    I’d also like to hear more about the hardware aspect of enotebooks. Seems like it would be critical to ensure that everyone always had immediate access. Realistically, what works (or doesn’t work) for that?

  26. james grayburn says:

    My former company (pharma) looked at a few of the commercial ELNs out there, and the general consensus was that of the 3 or 4 available, Symyx was good for medchem and process chem and had good integration with our in-house stuff, camsoft was good at medchem but too clunky and restrictive at other things- just wouldn’t handle the data we used, idbs was good at biology and as a nice general sketchbook, quite easy to use. We didn’t look at open source stuff as our IT guys thought it too risky, apparently
    I preferred the IDBS one, much more freeform and as I’m in pharmacology I found the others too restrictive.
    They all wanted to charge $$$$ for installation and configuration – guess thats where these guys make their money

  27. mr. gunn says:

    I’ve been dreaming about a good ELN package for some time, but haven’t been able to justify the expense, nor have I been able to get the slightest whiff of interest from my somewhat luddite lab group(They think Zip disks(remember those?) are high-tech, and a good way to distribute large files.)
    I’m leaning towards thinking that existing CMSes will branch into this area for small groups as soon as there’s sufficient demand.
    What I do is keep everything in Outlook Journal. This makes it easy to cut and paste into Office apps like Powerpoint and Excel, to share over the Exchange system, and to publish on the web. Not great, but adequate as is and approaching fairly good with a little VB programming.
    Note that this is only me in the group doing it, but if your group uses Exchange, it should scale OK.

  28. LNT says:

    At Wyeth we use Cambridgesoft ELN. It’s still being deployed to various groups, so many people are still using paper notebooks. So far, the Cambridgesoft ELN seems to be working well for us. I think that our IT group put in a little bit of additional functionality into the ELN.

  29. LNT says:

    One of the big problems with electronic notebooks (a few years back) was that they were inadmissable as evidence in court because the date and content could be easily changed at any time. Therefore, it was really not a good record of WHEN a particular compound was made. For those of you using informal applications (MS Office and the like), you should be aware that paper notebooks (when witnessed properly) have MUCH more weight in a court case than an electronic file does.

  30. zt says:

    I do med chem in big pharma. We evaluated ELNs from several major companies and found that Cambridgesoft’s product was far superior to the others, in terms of functionality, ease of use, and basically all measures we looked at. I am quite happy with it.
    In terms of drawing TLCs, one can use the Chemdraw TLC tool (by making a new tab on the experiment with a Chemdraw object), which you can use to reproduce just about any TLC. Alternatively, you can just record the relevant Rf. As a previous poster mentioned, it can be tedious to draw complicated looking TLCs with the Chemdraw tool, but most of the time I would imagine that it is faster than scanning and uploading a picture. Besides, how many of us really need to capture the exact shape and size of the spot, in what is generally a very qualitative art?

  31. TNC says:

    Does anyone here use digital cameras to record color, etc. of reactions as they occur? I suppose it’d be much more use in reaction development than anything else.

  32. skyywise says:

    My old industry job was at a mid-sized biotech in San Diego and they have an in-house electronic notebook, but the powers-that-be hadn’t done much to support it. The use of the electronic version was left to individual project discretion, and even then we were told to do a hard-copy notebook version in addition to the electronic. The rationale was: electronic makes life easier for us in-house, but the FDA may not like it because there is no standardized format, so we need to have our bases covered and retain hard copies. The result was that the tedium of notebooking was enough done once, and use of the electronic tool was left to the wayside. (Also see LNT’s comment above as to the ability of bureaucracy & administration to deal with a rapid change in technology.) This fear of not being able to get regulatory approval for the records was much more prevalent on the Development-side of R&D.

  33. guy says:

    i haven’t seen anyone yet mention it; but, i’ve been using the pacific n-west nat’l labs, ELN research collaboratory software; http://collaboratory.emsl.pnl.gov/
    for several years
    it is open source/ platform independent — functioning via webbrowser and small client.
    development has (apparently) ended due to funding lapse/termination … but the code is in sourceforge. http://sourceforge.net/projects/eln/
    we have found it to be easy to set up, use and maintain for anyone familiar with setting up a webserver.

  34. ppp says:

    We use ELN which is great for internal use but also make an hard copy printing and pasting the ELN. The latter is signed and countersigned as usual.
    As for the TLC problem I have to say that, sadly so, it will not be a problem in the future: new generation chemists tend to skip and rely upon HPLC-MS only…not knowing how much information they waste.

  35. Paul Norman says:

    I’m an undergrad in Engineering Physics, and we use paper lab books for our project course. I can’t really see going electronic, equations and sketches are a pain to do electronically.

  36. Ryan Sasaki says:

    Hi Derek,
    You mention how much your record keeping has improved and specifically the ability to attach all the data files (NMR and LC/MS)to your notebook records.
    I am curious, are you attaching actual data files? Is this raw data or processed? Is it just a PDF of the data or a scanned version?
    My experience is that attaching PDFs of the data appears to be the adopted standard for now. In addition, even in companies that have ELNs, I have noted a continued reliance on paper spectra for some.
    I’ve posted it at:
    http://acdlabs.typepad.com/my_weblog/2008/02/can-a-piece-of.html
    I’d love to hear yours and others thoughts on this topic.

  37. D says:

    I too was feeling like a dinosaur at 29,after finding out about this,so I gave it a shot using wetlab. It was great,timestamped experiments,procedures and protocols could be filled in before hand.Then guess what?
    It crashed mid experiment,I lost data,had to start over.I smiled and reminded myself “there’s a reason I stick to notebooks.As per tlc plates,sticking them in notebooks is good,but so is photographing them next to a ruler for scale.

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