Requirements for an electro...
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Requirements for an electronic lab notebook systemby elizabeth - 10:12PM, Jul 04, 2003 |
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We are investigating what it would take to bring Circus Ponies NoteBook into compliance as an electronic lab notebook for Mac OS X-based research labs (both commercial and academic).In particular, we want to hear from Mac OS X-based SciTech users regarding what they believe would be required to keep legally verifiable records of their lab work, such as what was written when, locking pages, affixing security dates/checksums, and having some sort of witnessing facility. Some preliminary research on our part has turned up LABTrack on Windows, an apparent leader, which uses the Surety system. But I’m not finding a lot of similar offerings on OS X.My questions to this group are:Is there a need for this kind of app or extension to an app like NoteBook? Are there existing apps out there that are currently filling this need just fine for SciTech users on Mac OS X?If not, what are some of the features that would be required to provide legal documentation of your work?Feel free to reply here or offline in a private message to me. If there is sufficient interest, I will provide a summary of the requirements I receive to the group in a future post.Thanks in advance for your input. |
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Hi- I think there is a need for such a system. Adobe Acrobat can provide support for this but I have not seen it used as such. The ability for the system to verify the user, a trusted witness, the original entry and any changes is critical as identified. If I could sign an entry with pgp or gnu-pgp and then optionally have a witness do the same this would go a long way towards getting what you need. Eudora and some other email programs have the hooks built-in for this function. Signing should also make the entry undeletable forn the notebook. An intersting extension would be to provide a truseted online signer for date/time. The only other feature that would then be key is to have a preference to force backups whenever a signed entery has been made to decrease the chance of loss. Joe
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Hi, I will just offer some random thoughts: - I would like to see a checkbox on a per page basis which would protect the contents from accidential editing - I like the use of a bundle for notebooks to keep all the parts together. However, this is a problem during backups which archive changed files when these bundles get very big. I would like an option to change the bundle to an ordinary folder to keep the size of the archived files down. This would at the same time open these files for easy access with other tools for example incorporating them in an index. - I think the links to attachments should be editable. I found an example of an implementation for content options that I liked in Workswell (In inspector: editable link, placement in the frame, scaling options inside the frame; and overall scaling by scaling the frame).
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I am trying to use Notebook in a laboratory situation and it kind of works but not in a true electronic form. There is nothing out there for OS X that I know and most PC lab software is so expensive that most academic labs can't begin to afford it. At the moment to be legal I have to print out each NoteBook page and put it in a real notebook. Even this would not fly in industry. The locking/security is an absolute must. So is the ability to fix the page layout independent of the window size. As in if you make the window smaller than your set page size you just don't see everything. It is easiest to tab delimit experiments as (very) free form tables but if your layout is dependent on the window things tend to get scrambled as the window size gets changed. The option of putting the dates inside each cell and the ability to display creation and change dates at the same time. Some idiot proof way of making the .nb files smaller or keeping all the bits together so we don't use so much space in nightly backups. Other things will come to mind.
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Lab notebooks need to be page to page consistent. Rigidly formatted except when you want to change it. aka having your cake and eating it too. Essentially we need a master inspector so that each new page is set up with the tab stops, date display, fonts, everything that can be set in the cell inspector. We often need to follow some one else's idea of what font to use and where the date goes etc. So having the ability to pre-define just about everything for the entire notebook or more accurately series of notebooks is very important. And then be able to override those settings when needed using the cell inspector...
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The main requirement is of course that is meets any "legal" requirements and I'm not really able to help to there (because I've never looked at them in detail myself and they are probably different here in Australia). But the other big requirement is COST. We are a non-for-profit research institute in an academic setting and don't have a lot of money to spend on extra software. People are happy with their paper notebooks (cheap) but I know quite a lot would jump at an electronic version that was affordable. I actually have to do some research for the IT committee on data storage and retention in Australia so if I come across anything useful I will post it here as well. Adrian Centenary Institute of Cancer Medicine and Cell Biology Sydney, NSW, Australia
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I use NB for my lab an project work. So far it does most of the things I want it to do. However, I have only to satisfy my own requirement. I do not have to document according to legal requirements. What I would like to see added to NB is this: - The ability to scribble diagram in a cell. So far I am using OmniGraffl and store the diagrams in NB. A light-weight diagramming feature in NB would be nice to have. <dreaming>Using a stylus on the trackpad of my iBook to draw in NB would be really cool.</dreaming> - I need the ability to export parts of my NB into HTML. I have to share my parts of my research. I would like to export a NP page to HTML format. Document that I have stored in NB should be downloadable on the generated HTML pages. So far I am maintaining two repositories, one in NB, and a set of HTML pages and other files in subversion. - I would like to see sort of a light-weight DEVONthing feature in NB. A feature that allows me to import text and pdf documents and have the content indexed. I tried DEVONthink but I don't like it. Handling is not really straight forward for me.
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I too post images in NoteBook created in OmniGraffle, Chartsmith, or LaTeX Equation Editor. Some ideas are best represented graphically. PNG or PDF import formats seem to work equally well. An important feature is the ability of NoteBook to accept images directly (that is, to import the image, and not just a link). This results in far fewer files to maintain. It also means that only the NoteBook file has to be secure. I am free to change or delete the graphics created with other applications and know that any previous version has been stored safely in NoteBook.
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I searched the postings for "patent" and came up empty, so I don't think this subject has come up yet. It would be absolute _great_ to have a certificat system (or whatever it might be called) to timestamp various things (pages?) to stand up to the maximum scrutiny (think multibillion dollar corporation with a small inventor's gun to their head). The way that engineers have traditionally worked (or _supposed_ to work) is to use a bound lab notebook with printed page numbers and a witness signature on relevant pages, stating "Read and Understood." I don't know how that varies from scientists' lab books. I do know that very few engineers use this system because of the difficulty in organizing their work in a way that makes sense to them rather than the lawyers. Notebook solves the single-organization problem quite nicely. One time about seven or eight years ago, I thought that Apple or someone else had introduced a certification system, but now that seems like a fuzzy memory, especially since there doesn't seem to be anything around now.
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Is there a way to put a heading at the top of each page? I am a prof in a med school and would like to have each investigator's name placed at the top of each page. Great program. Thanks.
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Isn't the page name displayed on each page of your notebooks? I thought it was on by default. If you open the Inspector (Menu "Tools", option "Inspector" or click on the small letter "i" in the lower right-hand corner of the page) and then select "Page Inspector" (the second icon from the left in the Inspectors icon bar, looks like a small page). Go to "Format" and then select "Styles". The top-most option should now be "Page Name". If you select it then the page will show a heading. Does that help? /Markus.
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quote: Yes, the page name is displayed but I would like to have an option whereby I can place the notebook owner's name at the top of every page. As the head of a lab with 6-8 people, I would like my team members to print out pages periodically and I will need to know whose notebook the pages came from. If there is a way to make a template, that might help or even define my own style (e.g., blank page with name at top), that would help. I see there is a discussion group for "The Great NoteBook Template Swap" but it is not clear how to make a true template.
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For Scientific Laboratory Notebooks: I see that you can "Prevent Editing" of the Cover Page (under the Page menu). If that could be extended to other pages, that would help scientists in protecting their data. I would suggest that you engineer it so that, as a default option, the prevent editing feature is activated for all pages except those created "Today". That way, you could not look at an earlier day's work and inadvertantly delete something.
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NB does not have a template function. I have a NB dedicated to hold "templates" (basically a set of pre-defined test procedures). When I need a "template" page then I copy it into the taget NB. Not too elegant but workable. BTW Did you already find the "Default" button in the Inspector? If you modify page settings, for example enable change dates and print them in red ink, then you can make that the default for all pages. Clicking on the small letter "D" in the lower left-hand corner of the Inspector window opens the "set page default" dialog. Regarding identifying the author of pages, did you consider using tabs to display the authors name? Do you just want printed pages? NB got an excellent "export to HTML" feature. I use that frequenty to share research with my peers. It is probably the most valuable NoteBook feature for me. Best regards, /Markus.
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The only other ways I could think of to identify the owner of a NoteBook page would be to set up each person's name as a keyword and assign it to the first cell on the page or set up a background image with the person's name at the top of the image and use that as the background for the NoteBook page. Just some ideas. Robin
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I thought about these ideas, too, but to put a cell with a name on every page requires the person to do that and I am trying to find a fool-proof way of doing this automatically. The image idea does not work because of how background images are placed (Tiled, Center, or Scaled). I tried various types of images to circumvent this but it just doesn't work right. Maybe this can be a function they add in the next version. If we could customize our own styles, that might work but I do not see a way to do that, either. quote:
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Hi, I am currently testing notebook for use in our lab as a replacement for regular lab notebooks. Of course, the main attraction is price, and in that respect, notebook is unbeatable. However I agree with most posts concerning lacking features. Must see features: - Any unmodifiable "signature/countersignature" system - Linking from text to cell and/or cell to cell which would make each notebook into a real hypertextual database on its own without index or TOC searches Desirable features: - "Master" stlyes or master inspector for entire pages or entire notebook but allowing individual cell variations when desired - Active scolling of an inserted pdf (basically being able to do what the inspector does when you choose which page of the pdf to show, but directly from the cell) Other than that, your app is very impressive.
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For those interested, you can see a competing system using Filemaker described by Petersen et al. Trends in Immunology March 1004 page 119 which the author makes freely available at www.immi.au.dk/mspetersen les K
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A quick update-- We still do not have the signature/counter-signature feature added to NoteBook. However the new Linking Framework enables linking (a) from one cell to another, (b) from text to a different cell, and (c) from text or cell to a web page.
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Hi Elizabeth, Thanks for the update. Presently, I cannot wait to upgrade to Tiger so the members of my laboratory can begin to use the Tables feature integrated in Mac OS 10.4. In addition to an unmodifiable "signature/countersignature" feature, I still would like to see the following features added: 1. Ability to add a header and/or footer that would print out on each page of a hard copy. This way, a scientist could mark each page with their name. 2. A feature that would eliminate the ability to edit the text of a previous day's entry. If this could be turned on/off with an administrator-type password that would be great. In addition, if you could still link text between a current day's page and a previous days text, that would be wonderful! George
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I have been using Notebook for over a year to keep my lab notebook--I am a postdoc in a Molecular Endocrinology/basic science lab. Everything we do now is digital--we haven't used a piece of film in over two years. Anyway, this notebook seems to work really well and the price is definitely an advantage over most LIMS systems. I have no specific legal requirements for documentation, so the security issues are not something that I can comment on. There are three items that I would like to see, however. 1) The ability to customize page headers--this has been commented on. I would like to not only have the page title, but be able to specifiy other information in general (say section title or researcher's name) but also put in page specific information. Specifically I would like to be able to put in a date that the work was done, and this is sometimes not the date the page was created (everyone look askance, I know I am the only person who might get a litte behind in keeping up the lab notebook). 2) I would like the ability to archive old sections of a notebook. Here's what I mean. I have my current notbook which is now several hundred pages long and over 100 MB in size. I can see that in a couple of years, this beast is going to get unmanagable with huge amounts of data from old projects, so the ability to get rid of this bulk, but still have it available will be important to me. Perhaps the ability to export sections of a notebook (as a notebook file) and then link to them in the current notebook would fit the bill. 3) The ability to import excel table (as formatted)--even as a pict graphic would be fine. Good luck with this one--Powerpoint can't even manage it. Currently I do web preview in Excel and then copy the charts as a graphic from the webpage into Notebook--I have found this to be more stable than trying to go from Excel itself, but not elegant. Anyway, just a couple of ideas. Michael
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It is hard to believe that it has been over four years since Elizabeth started a forum on using CP Notebook as a laboratory notebook. Frankly, without going into very much detail, I think Circus Ponies is missing a great opportunity to increase sales by adding some basic features to make CP Notebook more compliant for those of us in research. Some points in favor of doing this: 1. The use of Macs in biomedical science. Go to any biomedical research meeting and you will find that about 50% of the scientists there use Macs as their preferred platform. However, there still is not an electronic notebook avaliable with the simplicity of use afforded by CP Notebook. The few products that are out there are expensive to start with and generally require an annual license fee to maintain. Consequently, they are targeted to the pharmaceutical industry. The few I have managed to find are cumbersome to use and are not as well designed as is CP Notebook. 2. CP Notebook provides integration with many programs used daily in the laboratory and, with some tweaking, could be brought into greater compliance with the documentation needs of the scientist. 3. The general simplicity of the program makes it just slightly more complicated than writing in a paper-based notebook. Thus, users quickly master the data entry. 4. Besides serving as a receptacle for experimental notes, CP Notebook can be readily used to create web sites for information sharing among collaborating laboratories. It is also a great tool for collecting information when performing literature researches in preparation of writing a manuscript or review. So how about it? Anyone else feel the same way? G.
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I agree! CP Notebook seems to have stalled in it's development...I know I've been hoping to see some ELN features for a while now. -pauln@maine.edu
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I agree, too! I am a professor at a research university with a small lab. I have been looking for an electronic notebook to implement in my lab, and came across CP last week. In many ways, it seems suited for my lab, but many of the suggestions listed here would make it much better.In particular, a mechanism to lock pages to prevent further editing, and a way to make custom templates would be significant improvements. Thanks
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I work for a for profit company with lots of R&D efforts, and it would be great if we could use NoteBook for IP logging, eventually leading to patents or protection.
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For those that are interested in a LIMS system for there laboratory in addition to an ELN you might want to have a look at this website here: Your Lab Data - ELN and LIMS Your Lab Data is a free web-based LIMS (Laboratory Information Management System), aimed at a typical small molecular biology laboratory. It allows users to manage their chemicals, fridges, freezers, boxes, strains, plasmids or glycerol’s, oligos / primers and much more.
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I have just started to search (again) for a suitable type of electronic notebook. The Atrium Research site at http://www.atriumresearch.com/html/eln.htm gives a reasonably thorough listing of those that appear to be the top contenders (a few options are missing and a few URLs are now dead). They also have produced a document that analyzes results from a 2006 user survey on the use of ELNs (available for ~$2,000 - OUCH!). One theme that is now consistently promoted for ELNs is compliance with the Food and Drug Administration’s (FDA) Code of Federal Regulations (CFR) 21 Part 11 regarding electronic records and electronic signatures, electronic entry audit trails. Another is the ability to share/exchange notebook information, ostensibly by integrating the notebook front end as a client with a separate Web server / database system. Based on what I have seen so far, Notebook from Circus Ponies would be well-placed in feature/price ratio to offer an ELN. A focus on an ELN having many well-designed features for a limited or targeted market share would seem to be best IMO. Perhaps a "plug-in" framework would be a method to design templates for targeted audiences. Anyway, the general conclusions from the two Sept 2007 presentations on the Amphora site at http://www.amphora-research.com/news.html might be helpful in this regard. I also applaud Circus Ponies for the clarity of the information on their Web site - many of the competitors listed on the Atrium Research site just do not want to provide screenshots or documentation about their products without first collecting a user login.  Finally, alas, since I currently have to work on a WinXX system, Notebook is out of the running as a viable choice. I look forward however to picking up again on this thread once I return to the MacOS (in about a year).
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It looks like enthusiasm for the CP Notebook as an ELN has waned - any chance the developers can give us a hint if they might be working on this for release 3.1?
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What is the interest level currently of using NoteBook as an ELN? Would anyone who's interested please contact me at info @ circusponies.com? Best, __jayson
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I introduced Notebook in the lab for three Ph.D. Students on trial basis. It seems to works better than paper notebooks but still far away from being an ideal solution. Best,
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1. You can create a basic table via Format->Text->Inline Table. In the future basic math functions will be implemented in an update for tables. 2. I will add a Digital Signature to our list of possible future features. 3. An updated Time Stamp(Date Mark) is on our list, but I will let the software team know there has been another request. Travis
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The problem I see with electronic notebooks is the fact that things can be changed without leaving a trail of what was replaced. The most immediate problem I see with electronic notebooks especially in a life sciences situation is the danger to computers. I would NEVER bring my laptop into our lab. 1. It is a BSL2+ (deadly pathogens) lab. 2. Bench space is tight. 3. So much is going on in the lab, I often have a culture in one hand, a bunsen burner on, agar plates and tubes of media on my bench. It is hard enough trying to keep all the tubes upright. I would never expose my computer to that kind of environment. Everybody in our lab has a special “lab/dirty” pen to take notes during an experiment and a clean pen for notes at our desks. Since notebooks are legal documents, it would be important to have a record of things that have been crossed out and a way to ensure that a time stamp can’t be altered.
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Clare, in theory one could use Time Machine to keep track of precision changes to the notebook. It isn’t a perfect solution, of course, and in order to track all changes it wouldn’t work very well, as Time Machine is designed to cull backups over time. Another solution would be to continually archive your NoteBook (print > save as PDF, or export as HTML in order to get embedded files as well), which would generate snapshots in time. That’ll increase the disk space requirements quite a bit and introduces the need for some sort of archiving system, but it’s a possibility. I’m in immunology/molecular biology. I have a notepad that I use for writing down immediate data and notes, brief procedures, spur-of-the-moment ideas or ideas generated during meetings, and so on. NoteBook is used for “finalizing” things and putting it all into order. The ease with which I can find data compared to my paper-toting labmates is nothing short of incredible. And while I’ve seen some creative solutions for cataloging which reagents are used, nothing can beat downloading MSDS and technical data sheets, placing those PDFs into NoteBook, and then linking to them from corresponding experiment entries. That’d make write the “materials & methods” section of a paper a breeze for anyone, I’d imagine. Granted, I’m fairly certain that if we were to undergo some sort of audit to determine whether we can use my NoteBook file for patent disputes or something of that sort, it’d likely fail. I make my entries on notepages (rather than writing pages) and bulletpoint furiously, instead of using paragraph mode for each section of an experiment. This affords me lots of “date created/date changed” entries. I’m not sure how that would stand up legally, though… however, most of my labmates seem to have messy paper notebooks as well and I doubt that those could be used either. Not that it’s something to be proud of, but at least mine is organized and has some date logging! :) By the way, you mentioned a pen that’s resistant to ethanol – is it something that can be used to label centrifuge tubes? If so, would you mind sharing what brand it is? I have yet to find an ethanol-resistant marker, but it’d be pretty helpful…
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For chemical/water resistant pens- I really like uniball signo http://www.uniball-na.com/main.taf?p=2,2,3. For the centrifuge tubes I like VWR markers http://vwrlabshop.com/vwr-lab-markers/p/0011283/ For really important samples I use http://www.emsdiasum.com/microscopy/products/label/tough_tags.aspx?mm=23 Tough Tags (the plain white ones).
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jff
Member
07:00AM, Jul 07, 2003