Neil points out several advantages of ELNs, which I will paraphrase:

• Easily share data with lab members/collaborators
• Search experiments by date, title, keywords, tags
• Link experiments to related resources: “protocols, MSDS data, risk assessments, plasmid maps, PubMed entries, tagged data in social networks”

In a comment, Curtis says:

“While nearly every aspect of the modern research enterprise changes quickly, the lab notebook hasn’t changed in over 100 years”,

which he means as an indictment of the paper based notebook. I would take the opposite tack; If it has worked for 100 years or more, maybe we shouldn’t be so quick to throw paper based notebooks out.
The problem with ELNs is that they are inconvenient, compared to paper notebooks. ELNs require access to a computer to read or write. Also, it is easier to lose digital information, than paper and pen based information (I’ve had far more hard disk crashes than I care to think about).
Most laboratory computers aren’t at the bench, they are at the desk. Since they aren’t located where the work is occurring, there are three main options for writing up experiments.

1. Write up experiments completely before the experiment occurs, then perform the experiment just as planned.
2. Try to remember everything and type it up afterwards.
3. Write things in pen and paper, then transpose into the ELN.

The problem with each of these, respectively, is:

1. Things rarely go exactly as planned.
2. The longer between observing something and writing it down increases the possibility of errors.
3. Transposing information is twice the work, and also increases the possibility of errors.

In the real world, a mixture of all of these would be the way to go, but I think it is unlikely to be readily adopted by academic scientists, because of the hassle. Instead, I think we should try to leverage the work people put into their venerable old paper and pen lab notebooks with digital technologies.
One easy path to searchable, shareable notebooks might be Optical Character Recognition, where one scans in the lab notebook pages and lets the computer figure out what’s what, but this approach will be limited by how often a researcher drags the notebook over to the scanner.

An interesting alternative would be the recently announced pen-top computer from Livescribe. Basically, this is a pen that can “remember” what you write, and upload what you have written to a computer. I envision writing in my notebook, then when I (and the pen) get back to the computer, the recorded text is uploaded to the computer and “auto-blogged” into my ELN. Sure, it’s not perfect: any images I paste into my paper notebook wouldn’t be saved, and the formatting won’t be perfect. However, I could have a date and keyword searchable archive of the things I have written, from which I can then reference to my actual notebook.

If ELNs are going to come into common use, there are only two ways: forced by the industry/academic hierarchy, or so easy and simple to adopt that researchers would be fools not to start using it.

Learn from the iPod: it needs to be easy.

Updated comment

How to download a concatenated file of all H. influenzae genomes from NCBI Entrez Nucleotide

Note: I don’t know if this is the best way, just a way.

1. Go to NCBI Entrez Nucleotide.

2. Search for “Haemophilus influenzae [Organism] WGS” and get 576 results , 288 each from GenBank and Refseq. (”WGS” stands for whole genome sequencing, I think, but does not include completed genomes, for some reason.)

3. On the “Limits” tab, select either the “GenBank” or “RefSeq” results from the pop up menu titled “Only from:” to get the 288 GenBank records or the 288 RefSeq records. I am not sure which you should use, but I lean towards GenBank over RefSeq, as it is the submitted form of the record, so my example will proceed using the GenBank results.

4. From the “Display” pop-up, choose “FASTA”, and it will give you the FASTA of the first five results (Sorry, no static link available).

5. Next, choose to display a maximum 500 of the results, which gives us the FASTA of all 288 results in a web page format (Sorry, no static link available).

6. Finally, from the “Send to” pop-up, choose “file”, and your web browser should start downloading a text file of the results. .zip Archive of the resulting download (5 MB).

From here, you could probably use this file to make a BLAST database, however, there are 9 nearly empty FASTA records that should be deleted. You can do this many ways, but I like to do so graphically using the free TextWrangler, by the makers of BBEdit. To locate the empty records, I did a “find all” for “00000″, which are 5 zeros Once you delete these records, you end up with a multi-FASTA file containing genomic sequences from an additional 9 Hin strains:

22.4-21 (44 contigs), 22.1-21 (18 contigs), 3655 (23 contigs), PittAA (40 contigs), PittHH (59 contigs), PittII (25 contigs), R2846 (20 contigs), R2866 (4 contigs), and R3021 (46 contigs). I certainly can’t speak to the quality or completeness of these sequences, but you can download my results (.zip, 5 MB), if they would be useful.

I am sure there is some better way to do this, but I haven’t been able to find an FTP server where I can locate these files. A particular problem with this method is that it tends to slow your web browser to a crawl. I accomplished steps 4,5, and 6 with a liberal use of the Safari “stop loading page” button. Basically, I let the intermediate step pages begin to load, then stop them before they complete, so I can choose the next setting. With Firefox, I was unable to complete this tutorial, because the browser would become completely non-responsive for at least 10 minutes. Be careful!

Is there a better way to do this?

Color Oracle is a free software utility to simulate how the colorblind might see your artwork or figures available for Mac OS X (10.3.9 or better), Windows, and Linux. Another similar utility for this is Sim Daltonism (Mac OS X 10.2.8 or better).

According to Wikipedia article, as many as 8% of males and more than 1% of all people have difficulty distinguishing colors. We can make it easier for our audiences to interpret our figures and use our bioinformatics web applications if we give a little forethought and check to make sure that they will be able to discriminate what we identify with color.

Generally, I don’t use color in figures for journal articles or posters, but I do tend to use color in slide presentations. Now, I can make sure that my work is more accessible to those who might be colorblind.

Both software links above via Daring Fireball.

Update: I re-wrote this article and submitted it to MacResearch.org.

UPDATE—

The Wall Street Journal discusses how this is important for people’s names. 

When logged into MyNCBI, the words “Save Search” appear after you’ve done a query.

After clicking the link, a pop-up appears, letting you give your search a name:

You can access your saved searches from your MyNCBI page, which you can get to by clicking the “MyNCBI” link at the top right of any PubMed web page.
The popup also lets you choose to receive email updates to your search, which leads us to Tip #2.
2. Email the results of your saved queries
Save even more time in your searching by having NCBI send you regular updates to your most useful searches. New results of your saved queries can be sent to you by email daily, weekly, or monthly. You can even specify which day of the week you want to receive the results. This is a great way to keep up with topics without constantly reading journal table of contents.

You can modify these settings later by going to your MyNCBI settings page, which you can get to by clicking the “MyNCBI” link at the top right of any PubMed web page.

3. Save collections of results for later reference

Do you find yourself searching PubMed at home or at the library, but would like to use the results on your primary work machine? MyNCBI Collections can help.

When you get results from your queries, add selected items to the Clipboard, then you can save groups of items from your Clipboard as Collections, as part of your MyNCBI account. These collections are then available anywhere you login to MyNCBI, by clicking the link at the top right of any PubMed page. This feature make the very temporary Clipboard storage much more powerful.
Here’s a brief illustration (click each thumbnail for a screenshot):

1. After searching, send a subset of results to the clipboard:
2. From the Clipboard, send a set of items to MyNCBI Collections:
3. Give the collections a useful name
4. And you have a new Collection that can be viewed or exported later, anywhere on the internet:

4. Enable custom filters in PubMed with Filters
When researching a new topic, I am often looking for review articles and articles that are either Free Full Text or at my university’s library. With my customized MyNCBI Filters, articles that are reviews, free full text, or at my library are separated out into “tabs”. This can make it much easier to zero in on exactly what I am looking for, especially when under a time crunch.

You can select up to 5 filters for each MyNCBI service, and these can be enabled and configured from your MyNCBI settings page.
5. Add links to your library’s licensed online journals.
Enables the use of the your libraries electronic resources, directly from a PubMed abstract page. For instance, at the University of Wisconsin-Madison, this allows you to:

• locate an online full-text version of the article (if available)
• Check for this item in the library catalog
• Request a copy from other libraries, if not at UW

All this is done automatically, so you don’t have to type in volume numbers, journal titles, etc. This is particularly useful when you are traveling or working off-campus, where you would otherwise not have access to your university library’s resources.
To set this up:

• Go to your MyNCBI settings page by clicking the MyNCBI link at the upper right of any PubMed page
  
• Choose the “Outside Tool” link from the left sidebar of your MyNCBI page
• Select your library’s name from the long list of choices that appears.

Then, an icon for your libary should show up on any abstract page. Here is the one for University of Wisconsin:

Well, I hope I have revealed a bit of the power that you can access by registering for and using MyNCBI. I focused on PubMed, but any NCBI resource can be personalized using MyNCBI. Good luck!

PubMed offers Single Citation Matcher, which provides a great interactive interface to finding that article you need, and it’s available from the sidebar of all PubMed pages.

Basically, you start typing in any bibliographic information you have: the journal name, authors, dates, and/or title words. The interface even has autocompletion for the journal name and author names, based on number of citations.
PubMed even offers a helpful animated tutorial.

Then, there are 2 ways to use the bookmarklet:

• Highlight text within a webpage, then click the bookmarklet, and a NCBI search will be started using the selected text as the search parameters.
• Click the bookmarklet and a pop-up window will appear, into which you can paste your search term(s) or sequence. Click “OK” and the specified search will load in your current window.

1. Search Pubmed–The starting point for any biomedical scientific literature search.
2. Search PubMedCentral–A great tool to find articles that may only mention your term of interest in the discussion, methods, or figures of the paper.
3. BLASTN–Find nucleotide matches to your nucleotide sequence.
4. BLASTP–Find protein matches to your protein.
5. BLASTX–Find protein matches to the 6 frame translation of your nucleotide sequence in Genbank.
6. Search All Entrez–Find all references to a set of terms in all NCBI Entrez databases
7. Search Entrez Protein–Use accession numbers, protein functions, and other keywords to find proteins of interest.
8. Search Entrez Nucleotide–Use accession numbers, gene identifiers, and other terms to find nucleotide sequences.
9. Search Entrez Genome–Use variety of terms to find genomic sequences, integrated genetic and physical maps, and sequence maps.
10. Search Entrez Gene–Search the NCBI database of genes from RefSeq genomes.

Obviously, NCBI and NLM provide dozens of resources, but hopefully these search tools will be useful to you. I have tested these in Firefox 2.0 and Safari on Mac OS X 10.4.9.

These bookmarklets were adapted from those available at Jesse’s Bookmarklet Site.

This updated version only asks for your NetID once, and then remembers it thereafter. To reset the set NetID, double-click on the droplet, and enter the new NetID.

Download Attach to My WebSpace

AttachToMyWebSpacewas inspired by Sender, a product of Stairways Software designed to work with Interarchy.

Leave any other questions in the comments section or send me an email.

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University of Wisconsin-Madison Genetics Professor Sean B. Carroll, talks about evolution and the human genome. He’s the author of a new book, “The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution,”.

Science Laureates Town Hall : A discussion of the interaction of science and journalism by scientists and science journalists at Purdue University.