Electronic lab notebook

Hi all,

I'm starting on a new position soon, and thought I would start getting organized: having written my PhD thesis recently made me realize how hard it is to find the older things I've been doing. For that reason, I'm looking for an electronic lab notebook software: like keeping a good old paper notebook with my results clipped in it, and hand-written notes, but on my Mac. I've seen the web pages for Lab Notebook (http://www.macinchem.fsnet.co.uk/labnotebook.htm) and Labtrack (http://www.labtrack.com/), but I'm neither impressed nor eager to try them...

What do you use? What have you tried?

PS: To give more insight, here's what the dream app would be:
* easy copy-pasting/drag 'n drop
* ability to re-open the files
* metadata and search (tags, keywords, ...)
* possiblity to link to older notes and graphs
* store PDF (or TIFF) representation of external files along with the original file: preview files without their originating application
* automated backup mechanism
* encryption on disk

Things that can be important to some people, but which I don't consider of primary importance for me:
* any kind of certification, digital signing, etc.

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try journler

You should have a look on the application journler http://journler.com/.
It's not specifically made for science purpose but that shouldn't be a problem. It has note taking, file managing with keywords, embedding of external files and many other features. also it's free.

journler

Yup, I just started using journler too, a few weeks ago. The only thing it won't do for me is export attached files when I export entries. Journler is scriptable so I should be able to make my own export format with an AppleScript, but I haven't gotten around to it yet.

Electronic Notebooks

Most of the major players in the area are moving away from desktop applications to client server architectures with all the data stored in a SQL (usually Oracle) database on a remote server. This is obviously great for the big corporations who are willing and able to pay the multi-million dollar price tag. Do you need 21 CFR Part 11 compliance?

You could look at

Notebookmaker http://www.notebookmaker.com/
ORNL http://www.csm.ornl.gov/~geist/java/applets/enote/ (Not updated recently)
There are also and open source projects
http://www.opensourceeln.org/Members/webmaster/core/front.txt

Also have a browse around here

http://www.iqpc.com/cgi-bin/templates/genevent.html?topic=237&event=13555&

File obsolescence; also Notebook and DevonThink (Pro, Office)

Notebook (Circus Ponies) and DevonThink (Pro and Office) should probably fall under your gaze. DT Office has OCR in it which is nice for those papers that are PDF bitmaps.

On another note--I would be careful to not select something that uses a file format that might become unsupported at some time. You might not be thinking of it now, but for a person whose career spans decades this is a very serious consideration. I wrote my dissertation as well a whole lot of other things in FullWrite Professional (still the greatest word process of all Mac time). Fun while it lasted, but I still need to look at some of those old files (letters to patent attorney, e.g.) and OS X on a G4 is the last gasp because the Intel processors do not run Classic, as I understand. (I wish I could figure out how to write a script to automatically convert them all to Postscript rather than do it all manually.)

I now have an aversion to single-source file formats. Some of these notebook programs store their goodies in a package so you can still get at them, but who wants to convert GB's of data by hand when the developer dies or loses interest in his program? Also, many of them can export as a web site which is pretty nice, and maybe all you need in the long run, but again, that's a gamble.

As for your original question (what notebook) I'm holding out hope for the Finder in 10.5--it is supposed to have a preview feature. What I'm hoping for is that Apple has the sense to provide a plug-in feature so that app makers can write a preview plug-in for their non-standard files. In the meantime, Path Finder has a decent preview feature for some file formats.

Electronic Lab Notebook

We're actually writing an RFP for electronic lab notebooks now.
We're looking for an enterprise solution with an rdbms back end and cross-platform friendly interface.

I too would be concerned with proprietary file formats. You are apt to get stuck trying to convert them to something portable sooner rather than later...

I'll post updates as our process moves along for selecting a product.

Enterprise Lab Notebook

I'm sure many people would be interested in hearing about your efforts.

The issue of proprietary file formats is a concern, not just for the notebook but also for all those diverse applications that scientists like to use. Whilst some have open standards many are closed binary formats. In a project I was involved with we ended up having a print to database that saved a pdf version of the output. Not ideal but it was hoped that in the worst case it could be read and rekeyed if needed. MacOSX was rather nice in that it was easy to install in the PDF button in the print dialog.

Wikis

You might consider some of the Wiki options available. Gina Trapani makes the suggestion to try installing your own Wikipedia (which supports LaTeX) or Instiwiki. See Hacks #4 and #5 from Lifehacker (Chapter 1).

There are also lots of TiddlyWiki options developed explicitly for this. TiddlyWiki is light weight, simple, flexible, and can be stored on a flash drive. Oh, and because it's all done in JavaScript accessed via any modern web browser, it's portable. These TW lab notebook options often include the jsMath plugin which allows LaTeX to be used within the Tiddlers.

One old favorite is TiddlyWiki Student Edition (SE), which may or may not be useful for general lab note taking.

If you do more TiddlyWiki searching, you might find lots of options that work for you.

All of that being said, there's also the OpenSource Electronic Lab Notebook.

--
Ted Pavlic
http://www.tedpavlic.com/
http://phaseportrait.blogspot.com/

Wikis

You might consider some of the Wiki options available. Gina Trapani makes the suggestion to try installing your own Wikipedia (which supports LaTeX) or Instiwiki. See Hacks #4 and #5 from Lifehacker (Chapter 1).

There are also lots of TiddlyWiki options developed explicitly for this. TiddlyWiki is light weight, simple, flexible, and can be stored on a flash drive. Oh, and because it's all done in JavaScript accessed via any modern web browser, it's portable. These TW lab notebook options often include the jsMath plugin which allows LaTeX to be used within the Tiddlers.

One old favorite is TiddlyWiki Student Edition (SE), which may or may not be useful for general lab note taking.

If you do more TiddlyWiki searching, you might find lots of options that work for you.

All of that being said, there's also the OpenSource Electronic Lab Notebook.

--
Ted Pavlic
http://www.tedpavlic.com/
http://phaseportrait.blogspot.com/

wikis

I have considered Wikis and blogs too. One advantage to the web based tools is that you can use wget or some other program to download static html pages of the entire site that are viewable without the database and webserver. I suppose html will survive file format obsoletion longer than anything else.

Another Mac ELN to try

You might try the CERF-Notebook™, which runs great on Mac OS X and Windows. Made by Rescentris, it offers all the features you ask for as well as full 21CFR11 compliance, audit trails, etc. It's in use by many academic as well as commercial (pharma) organizations.

My ResearchWiki

Let me take this opportunity to second using wiki software.

http://www.cmms.pitt.edu/~albert

Using the wiki has provided the following advantages
- no compatiblity issues: because it's a web-page nearly every operating system and browser will display the information exactly as intended
- complete history of every page (and uploaded file): if it appeared once on the wiki it will never be lost
- extendable: Almost anything is possible with simple php extensions (i.e. embed flash movies, bibtex support, enhanced security features, and I have just replaced the search function with Google Custom Search)
- collaboration: wikis can be setup for multiple users to edit, or using the discussion features. Users also have private sections that only they can edit.
- journaled entries: traditional dated entries can be kept and searched

For me, using the wiki has changed the whole concept of a lab notebook. No longer am I forced into a daily journal of my activities with information scattered over weeks and months of entries. Now, consistent information is presented which forces me to think beyond just collecting data and writting it down.

Albert

Leopard Server's Group Wiki

I agree completely with you Albert -- that's one reason that the "Teams" features in Leopard server look so compelling. You can set up group calendars, wikis and blogs very quickly for yourself or the research group.

As soon as Leopard server is released, I'll have a walk-through of setting up a group wiki for my group. A few key additions to your list for a good lab notebook or wiki IMHO:

- Attachments (i.e., being able to attach graphics, data files, program archives, source code, etc.)

- Authentication: one key requirement for paper notebooks as well as electronic lab notebooks is authentication and signing (e.g., for patent or legal requirements).

But as you said, a wiki is great for collecting information and keeping it organized. Being able to link between multiple entries is very useful.

OmniOutliner

Have you seen OmniOutliner http://www.omnigroup.com/applications/omnioutliner/

Labbook

If you have experience with LaTeX, try the labbook package (http://tug.ctan.org/cgi-bin/ctanPackageInformation.py?id=labbook).

Copy and paste is a given and since files are stored in ASCII text, they can be reopened for millennia to come. If you use pdflatex to publish the lab notebooks, you can use all of the metadata associated with a pdf. You can also take advantage of link creation for pdfs to link to older notes/graphs.

You'll have to take care of your own backups, but if you use an automated backup system that task isn't too onerous. Finally, you can use Disk Utility to save files in an encrypted DMG.

Matt Kizerian
Systems Engineer
ReliOn, Inc.
www.relion-inc.com

TiddlyWiki Plugins

Hi,

What TW plugins do you have running?

Dan.

New Labbook approach

I have just prepared a new E-Labbook system. It's and integration between Wordpress (for Lab Blog) and phpBB (for labbok).
You can find some information at my site www.francescocimino.it
Actually my siste is under construction so just few information are reported. However I'm just preparing an HOW-TO build an e-Labbook.

Francesco

Electronic lab notebook

One possibility (shameless plug, but actually on topic...) if you use Mathematica--which is required for it--is my product "A WorkLife FrameWork":

http://Scientificarts.com/worklife

Send me a note if you have any questions... there's a trial version).

David Reiss
http://Scientificarts.com/worklife

Leopard Server Wiki/Blog as Research Notebook

Not sure if anyone is still checking these comments, but I thought I would post my experience using Leopard Server's wiki/blog server as my electronic research notebook. Here is my setup:

-- laptop installed with Leopard Server (hosts wiki/blog)
-- have both a wiki (all research notes) and a blog (daily monitoring... heavy with links to wiki pages)
-- also use to store notes on talks, etc.
-- if my laptop is on the network, then I can access my research notebook through a browser from my other work machines... this makes importing results/plots/code/etc. very very easy.
-- why a laptop? I can use the wiki/blog even when I am not plugged into the network and I pretty much take my laptop everywhere I go anyhow.

I love it. I have completely switched over. For equations I use LatexIt or screen shots from Mathematica, etc. The OS X Server wiki is my favorite because I didn't have to learn a special wiki language... just normal HTML. Inserting figures is incredibly easy. It looks fantastic and is extremely usable on a daily basis. Searching is great, keywords work well, etc.

My last "To Do" is to enable a calendar server on my laptop as well so that I can store calendar items and to-do lists on the same wiki.

Great thread on ELNs! Check

Great thread on ELNs!
Check out this website with more ideas
www.e-lab-book.com

Not much on Macs yet, but some universal stuff.

diary / notebook

Try zengobi's "Curio" or Eastgate's "Tinderbox" or "Devonthink Pro Office". They have different strengths/weaknesses but are the best of the bunch.

voodoo pad

Today I discovered VooDoo Pad (VPD):
http://flyingmeat.com/voodoopad/

And their software is excellent. It has a lot of nice features, including the ability to easily drag-drop stuff from other apps, interface with Safari to easily collect URLs in VPD, has a wiki-like structure that's easy to manipulate... etc.

Anyway, I'm a fan.

e-CAT; new online eln

Thought the forum contributors might like to check out e-CAT. e-CAT, which has just started beta testing, is the first dedicated online lab notebook specifically designed to enable academic lab scientists to conveniently document experiments and manage data online. e-CAT has the following features:

• A GUI with the look and feel of a lab notebook
• Web data entry
• Collaboration support: groups, permissions, data sharing
• Commenting on, signing and authorizing experiments
• Scalable data management for tens of millions of records
• Flexible, user-configurable database design and restructuring
• Powerful, rapid and effective search
• Image management for an extensive range of commonly used scientific file formats
• Full support for IP and regulatory compliance

And its available at the bench! You access e-CAT through a web browser so you can use an iPhone or iPod touch to enter data into e-CAT.

You can watch the intro videos and sign up for the beta testing at www.axiope.com.

EverNote

I'm a PhD student, and I've been using EverNote for a year. I love it. I log everything in there, from recipes to unfinished thoughts to official research notes. When I graduate, I will export all my lab-tagged notes to PDF and leave them with my group.

The software even searches out and indexes text and handwriting from images. You can also snap pictures directly to it from your iPhone, it integrates with Google Desktop search, and you can access your notes from anywhere you have web access (online sync). I've even snapped photos of whiteboard scribbles, and it searches the words as if I had written them on a tablet PC.

You can put todo checkboxes in any note, and it has full RTF capability for documents, etc. This software includes a web clipper, print screen capture, tagging, etc. No problem.

It's great, but if you can find something better, I'd love to know.

ConturELN as a service

ConturELN is now available as a service. This ELN is widely used in academia and industry. It will be free for single users.
http://www.contur.com/products/conturelnservice.asp

OneNote replacement?

New Mac user here, looking for a replacement for Microsoft OneNote, which I use for class notes and as a research notebook. I looked through all of the great suggestions posted in the comments, and think Evernote and ilabber(CounturELN) look the most interesting. Anyone have pros/cons on these or other programs as compared to OneNote? Thanks in advance.

Re: Electronic lab notebook

I generally live inside of Mathematica. So I wrote an add-on package for Mathematica that, amongst other things that allows you to keep Mathematica as the focal point for your work, has a Diary functionality (which is, in effect, a context for a lab notebook).

See http://Scientificarts.com/worklife for some information on this.

David Reiss
http://Scientificarts.com/worklife

IgorPro

Dear All,

I see the advantages working in Wiki's. But my own productivity is much higher, if I do the reports within IgorPro (www.wavemetrics.com). See also http://www.wavemetrics.com/products/igorpro/notebooks.htm.

Best regards

Stefan

ilabber not for mac

Whoops, I got through step 4 of ilabber registration and found out the program is Windows only. I was hoping to avoid buying Parallels...

Google Sites

If you're looking for something wiki-like, but don't have your own server, there's Google Sites. You can make your site private, and you can insert different kinds of content, including images and videos. If you also set up a Google Docs account, you can compose reports locally, upload them to Google Docs, and then insert the Doc into Google Sites. I don't know if it will handle equations through Google Docs.

It works well for my purposes, because we still keep paper notebooks -- with carbon copies stored in binders -- so we have multiple redundancies in case of data loss. I've heard that Google will eventually incorporate archiving and downloading features, so that will allow even more redundancy. My students are Facebook addicts, so they are quite at home with web-based tools.

The disadvantage is the possibility that Google will somehow leak information that you don't want circulating, but the risk is so small for me that I'm not too concerned.

— Simon

ELN

One of the most important things for me is to have corresponding datasets available to work with easily. It may be a little off the wall, but I chose Bento to be my 'notebook'. Supports drag and drop of any figures I want, takes notes, arranges spreadsheet data and links in nicely with iCal, AddressBook, and Mail to keep tabs on when I do things, who I collaborate with and what we talk about. It supports exporting to excel and numbers as well as CSV so I can import to a SOL server for some heavier number crunching. It's basically mini-filemaker (just for Mac though).

MAC-friendly alternative to ilabber

Rory Macneil

We have just released eCAT, an affordable online electronic lab notebook that is MAC-friendly and runs in all major browsers, including safari.

Enterprise Lab Notebook

The issue of proprietary file formats is a concern, not just for the notebook but also for all those diverse applications that scientists like to use. Whilst some have open standards many are closed binary formats. In a project I was involved with we ended up having a print to database that saved a pdf version of the output. Not ideal but it was hoped that in the worst case it could be read and rekeyed if needed. MacOSX was rather nice in that it was easy to install in the PDF button in the print dialog.
Aprilaire Humidifier | Aprilaire Humidifiers | Aprilaire

ELN Directory

I work in the pharma industry developing and implementing LIMS. As a hobby and to keep up with new software, I maintain a LIMS directory. A few months ago, I started adding ELNs to this directory. I was searching for ELNs to add to this directory when I came across this site.

You will find some that are not listed above: Symyx and Nexxis for starters.
ELN Directory

I can not offer input as a user of an ELN, just LIMS.

__
Bruce N

iPad ELN

Useful list, I note there is an iPad ELN (http://www.ipadeln.com/).

a journal is meant to order entries BY DATE

Dear all,

reading all the previous entries, I started to wonder if I am the only one that wants to have more control over my data... I had a look at many of Your suggestions - but none of them meet my (relatively simple) needs: what I'd like to have is sort of an iTunes that would allow me to order my data and notes. A central issue would be to keep all data in a clear hierarchy, simply made up of folders - typically by year, month, day. The folder for one day would then contain ALL measurement data and lab notes to those data, and probably some plots I made from that data, and some metadata to interconnect the respective entries. Within the program, I'd like to be able to have a look into my folder, have a CONVENIENT look at my lab notes, and open my plots within the software - preferably using an effect similar to Apple's Quickview (so that I'd have my data LARGE on the screen to look at - not just within a subpart of the window, where I'd have to scroll around to see it. Additionally, it would be nice to open data from the software within specified analysis software I often use (such as Gnuplot or plot, to name some).
I think that that's what would really help. However, what I see here are lots of programs that create NEW documents out of documents that are already existing - and store them inconveniently in a proprietary folder structure that's completely unclear and not portable. My suggestion would have the big advantage that the data folder could also be used and understood by someone who only has the Finder - or, God forbid, a Windows PC (!) - or, of course, Linux or another UNIX system (good friends!)...

What do You think? Wouldn't that be great to have?

Thanks! Kind regards,
Björn