Digital Upgrade

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May 1, 2010
Amber Dance

Digital Upgrade

How to choose your lab’s next electronic lab notebook

The bound, graph-lined laboratory notebook has long been the quintessential scientist’s accessory. But large digital data sets, such as the sequences of hundreds of genes or the results of high-throughput assays, hardly lend themselves to a pen-and-paper format. Enter the electronic lab notebook (ELN), incorporating all your sequences, graphs, and images into a single place.

Pharmaceutical companies have been using ELNs since the 1990s. More recently, academics are beginning to dip their toes into the digital datastream. The benefits are numerous—from the ability to copy and paste common protocols to keeping track of experiments as lab members come and go. “Your biggest enemy when you have a laboratory is the turnover of postdocs,” says Robert Damoiseaux, scientific director of the Molecular Shared Screening Resources at the University of California in Los Angeles. “The post doc is gone—where the heck is the data?” With a searchable ELN, there’s no more paging through musty old notebooks or hunting for ancient freezer boxes. Many ELNs store data in HTML or related formats that should remain readable in the future.

ELNs also save time. David Zimmermann, CEO of Kalexsyn, Inc., in Kalamazoo, Mich., estimates that scientists at the company spend 25 to 30 percent less time on data entry since they switched to an ELN. And taking notes online allows scientists to share data with scientists at the next bench—or across the globe. Many ELNs run within a Web browser, meaning you can access them from any computer or smartphone. For those doing patentable or FDA-regulated research, ELNs offer the ability to electronically witness entries and track the date of every edit, ensuring an audit trail.

Ready to ditch the paper notebook? “Go ahead and accept it, it’s going to happen anyways,” says Robert Parkhill, director of operations at VAX Design Corporation in Orlando, Fla. But with numerous ELNs available—from free apps to off-the-shelf software to customized commercial systems—it can be hard to wade through the choices. Options range from general-purpose note software to ELNs specialized for drug discovery or electron microscopy. Some ELNs are best for small groups, others are designed for hundreds of scientists to share. You may want to host your own data server, or rely on your ELN provider’s. Make sure you understand how entries are secured from later tampering, so you can use the notebook as legal proof if needed.

Those who have made the switch say the perfect solution does not yet exist, and it’s essential to examine your options closely. “You want the notebook to adapt to your workflow, not your workflow to adapt to the notebook,” Zimmermann says.

Here, The Scientist profiles a few of the ELNs out on the market.

LABTrack (www.labtrack.com)

Features:
An early entry into the ELN market, LABTrack, LLC, based in Lake Forest, Calif., has been around since 1997. “It functions just like a word processor; it looks a lot like Microsoft Word,” says CEO Richard Stember. Users can build their own forms for data entry, adding custom fields such as “cell line” or “dosage.”

Best For:
LABTrack is a general-purpose tool for all kinds of science and any size lab.

Pros

  • The word processor design is easy to use, says user Gary Eden, a chemist with the VA Cooperative Studies Program in Albuquerque, N,Mex.
  • It’s easy to customize. “It’s probably the most flexible system,” says Parkhill, whose lab uses LabTrack in its work testing vaccines.

Cons

  • Parkhill says he sometimes has to call for technical assistance in figuring out advanced features.
  • LabTrack is not specialized for specific disciplines like some other ELNs.

System Requirements:
LABTrack uses a Web browser interface. The computer or server you store the data on must be running Windows.

“It functions just like a word processor; it looks a lot like Microsoft Word.”

Audit Trail:
Completed entries can be locked, and every time content is modified, the program encodes the author, date, and time. LABTrack uses the same hash codes that police and the FBI use to prove that no one has modified digital evidence.

Cost:
Price is based on a sliding scale depending on the number of users. A team of 10 would pay $11,000 if commercial, $9,350 if academic. An alternative monthly subscription service starts at $30 per user.

ConturELN (www.contur.com)

Features:
Contur Software, AB, based in Stockholm, Sweden, markets ConturELN for multidisciplinary laboratories that integrate both biology and chemistry. Biologists see the features they want, such as easy annotation for images; chemists see features specific for their work, such as chemical drawing tools. Contur also hosts a “lite,” browser-based version called iLabber, used mainly by smaller groups.

Best For:
Large and mid-sized commercial labs doing multidisciplinary science.

Pros

  • “It’s incredibly quick to learn,” says user Stuart Sealfon of the Mount Sinai Medical Center in New York City. Researchers in his lab model molecular networks.
  • The program is adaptable to users’ specific needs, with add-ons to collect data directly from scientific instruments or manage chemical reactions.

Cons

  • Managing ConturELN may be too much work for a researcher alone, says Sealfon, who relies on the Medical Center’s IT staff.
  • The search function could be improved, Sealfon says.

System Requirements:
The software runs on Windows; the data is stored on your own server.

Audit Trail:
Once written, entries can be locked to prevent future modifications. An errata section allows for corrections. Digital signatures are built in.

Cost:
$1,000 per user annually. The iLabber program is free for single users and $60 per month for up to 20 commercial users; academic labs get 50% off on iLabber.

Features:
The iPad ELN (no relation to Apple’s tablet computer) was initially developed by researchers at Paris’s Institut Pasteur and is now sold by Cognium Systems, also based in Paris. The goal, says product manager Alexander Polonsky, was to design a middle ground between a wide-open text editor and rigid forms that don’t allow for variation in input. It’s difficult to compile related data from freeform notes, Polonsky says, but unchangeable forms may not fit every experiment. iPad is based on categories called “tags,” such as “participant,” “experiment” or “method.” Within each project or experiment, users can select the tags they want to use—rather like building a custom form for their particular needs that day.

Best For:
Any kind of science in academic, government, or small commercial labs.

Pros

  • The system is easy to use and customizable by adding or deleting tags.
  • Two or more collaborators can work on the same experiment, as long as they are not editing the same tag simultaneously.

Cons

  • The iPad ELN only allows certain tags in different documents, says user Adrien Six, an immunologist at Université Pierre et Marie Curie in Paris.
  • Granting and denying users data access can get complicated because you have to fine-tune who has read-only access or editing ability on each project. That complexity may turn off some users, Six says.
“You want the notebook to adapt to your workflow, not your workflow to adapt to the notebook.”

System Requirements:
iPad editors are available for Windows, Mac, and Linux computers; there is also a read-only browser version. Data are stored on your own server.

Audit Trail:
Each tag notes who last modified it, and when. Users can link iPad with third-party software that supports electronic signatures. Scientists can print out notes related to intellectual property.

Cost:
40 euros ($55) for each user license.

OpenWetWare (www.openwetware.org)

Features: For a DIY ELN, think wiki. OpenWetWare, started by students at MIT, is now a global community of laboratories led by a volunteer committee. It uses the same MediaWiki software as Wikipedia. OpenWetWare requires sharing—anyone can see what you post. The format may incite fear of being scooped, but it shouldn’t, says Steve Koch, a biophysicist studying molecular motors and DNA-protein interactions at the University of New Mexico in Albuquerque. “If you’re completely open, you’re all over Google,” he says. “There’s no way someone could accidentally steal your idea.” Some researchers do keep data private by hosting personal versions on their own computers.

Best For:
Any scientist comfortable with open notebook science.

Pros

  • The format is unconstrained—you can set up any categories, and as many users and pages, as you want—and fast to set up.
  • Open notebooking attracts collaborators. Koch counts three collaborations that wouldn’t have happened if he weren’t on OpenWetWare. And his students build professional networks well before they author a paper.

Cons

  • Wikis were not designed with scientific data in mind. For example, it’s hard to make a table, Koch says.
  • Open notebook science “does limit where you can send your work,” says Jean-Claude Bradley, a chemist at Drexel University in Philadelphia, who also uses an open wiki notebook. His lab sticks to journals that accept preprints.
  • Posting online voids international patent rights, although US patents are still possible.

System Requirements:
All you need is a web browser. OpenWetWare hosts the database and takes care of backups.

Audit Trail:
Any registered user can edit a page. However, the wiki tracks when edits are made and who makes them, so it’s easy to revert to an earlier version if necessary.

Cost:
Free

There are many ELNs available. Other options include, but are not limited to:
ELN Best For Features Access Server Cost
eCAT Academics and small corporations; any discipline Enter data in an empty page or complex, customized template Browser Yours or theirs Small academic labs will pay $1,000 and up; large commercial users will pay up to $18,000
Symyx Any lab One general and six discipline-specific versions Browser or client Yours or theirs From $100/user/month to multimillion-dollar installations
Sciency Any lab Integrated with databases such as GenBank Browser Yours Academic $7,999; commercial $11,499
Rescentris CERF Any lab, primarily life sciences Integrates with other programs such as Excel Client; “lite” browser version Yours or theirs Commercial $2,500/user; academic $1,250/user
E-Workbook Any lab Biology and chemistry versions Client Yours Depends on the lab
NoteBookMaker Any lab Simple format that mimics paper notebooks Browser or client; based on FileMaker Yours or theirs Academic $2,800 or $99/year; commercial $4,200 or $149/year
Collaborative Drug Discovery Labs assaying small molecules Three versions differing in privacy level Browser Theirs Between 4 and 5 figures, depends on the lab