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LabArchives, Electronic Lab Notebooks, and Education

As those of you who follow scientific education are painfully aware, the U.S. has slipped dramatically in the production of capable scientists.  According to Mariette DiChristina, Editor-in-Chief of Scientific American, “American students are now ranked 22nd and 31st among their international peers in science and math, respectively.”   In order to help improve the situation, last May, Scientific American, along with its parent company, Nature Publishing Group, launched a program entitled “1000 Scientists in 1000 Days” which is designed to connect volunteer scientists with K-12 students to advise on curricula, answer a classroom’s questions, or visit a school.

LabArchives, maker of one of the leading and most innovative Electronic Laboratory Notebook (ELN) software, applauds this effort and has also launched a parallel program to help bring improved information technology into laboratory courses taught in both K-12 and undergraduate institutions.  Now called the “LabArchives Student Edition”, our new product includes virtually all the power and features of our Professional Edition at a per student cost that is less than that of a paper notebook.  LabArchives Student Edition has been in Pilot for the fall semester at a number of leading colleges and high schools throughout the US, and we have been enormously gratified by the reception from both the students and instructors.

Not only is LabArchives Student Edition “green”, it improves the experience of the students by being simple to use and accessible from anywhere.  In addition, like our Professional Edition ELN, LabArchives stores every version of every entry that is made into each Notebook.  Not only does this teach the proper application of the scientific method, but it is more fun to use, saves trees, and reduces our carbon footprint.  Perhaps most importantly, the built-in collaborative features of LabArchives enables instructors to more easily review and grade the work performed by the students.  Instead of having to collect 20-100 paper notebooks at various points throughout the term, bring them home, grade and comment, and return to the students, the instructor can, at any time, view the work that is done and make appropriate comments from any computer that is connected to the Internet.  This often enables instructors to provided needed guidance along the way…well before a student has gone astray.

The LabArchives Student Edition Pilot will continue through the 2011-2012 academic year, and we welcome new participants at all levels.  For more information, or to enroll in the program, please contact us at

LabArchives is proud to be participating in a nationwide effort to improve the performance of students in science and math, and are devoting significant resources to enhance our leading electronic laboratory software to provide even better functionality for this market.

LabArchives and “doi’s”

LabArchives is especially excited to announce the addition of  doi’s to our flagship product.

But “what is a ‘doi'”, you might ask? And what does that have to do with my laboratory data?

DOI is an acronym for “Digital Object Identifier”.  Most people are familiar with doi’s from reading journal articles, most of which include a Digital Object Identifier.  For journal articles, this is a permanent (or “persistent”) identifier that enables readers to locate the online version of an original article.   You can do so by going to sites such as or

The doi system was created and is managed by The International doi Foundation (IDF).  It was born out of the need to establish persistent identifiers for a wide variety of digital information, including publications and data.  Unlike URL’s, which may change, or vanish, a doi is “forever”.  Only select organizations, now including LabArchives, may assign doi’s, which are managed by the IDF.

So…back to LabArchives.  One of the most powerful features of LabArchives is the ability to easily share selected data:  Within the lab, with collaborators, or with the entire world.  This function has always been available through the assignment of a URL;  now, users can assign a “DOI” to any collection of data and make it available in much the same way.

In addition, with our new doi system, a user can choose to share a data set as it exists now, or they may enable users to continue to view changes as they are made.  For example, if you publish a paper and want to make all data related to that paper available, you can assign a doi configured to make it available as of the time the paper was written.  You may then continue with your research, but viewers will not be able to see any new results (until you choose to make them available).

Why is this new feature so important?  Among other reasons, the National Science Foundation (NSF) recently mandated that all NSF funded research must include a plan to share all data after a suitable embargo period.  This can be an odious task:  Scientists must attempt to gather all files, observations, notes, etc. and find a “repository” to which they must then upload all their data.

Not so for LabArchives users;  all (or select) data in any Notebook is ready for sharing.  Simply assign a doi to those data of interest and you are done.

LabArchives Features new Viewer for Office, PDF, and Text

LabArchives is excited to announce the release of a major new capability that greatly enhances the utility of the leading Electronic Lab Notebook (ELN).  While LabArchives has always provided for the ability to store any type of files within Notebooks, the new viewer feature, released over the weekend, now provides the ability to view Office, PDF, and text documents in their entirety without the need to launch any additional software.  Both existing and new documents are automatically compatible with the viewer, so even Notebooks that have been in use for years will immediately benefit from this new feature.

Here is an example of a typical file in the context of a Notebook:

Sample PDF

PDF file shown in the LabArchives viewer

Using the left and right arrows, one can now navigate through the entire document without leaving the Notebook page on which the file appears.

The current version of our viewer works with PDF’s, Microsoft (both 2003 and 2007) Word, Excel, and Powerpoint documents and Text files.  Our plan is to continually add support for additional scientific file types, with the ultimate goal of providing the ability to view a wide range of scientific data without ever leaving the LabArchives Notebook.  As always, we welcome the suggestions of our users for file types that they would like to see supported by our Viewer.

As you may know, last month we released our new LA Docs features, that also enables users to create and edit Office docs directly within their Notebooks.  Combined, these features move us closer to our goal of providing a central “hub” in the laboratory, so that our users may conduct all of their research…including planning, experiments, collaboration, and publishing…all from within the LabArchives platform.  Through features like these, as well as collaboration with other leading vendors of scientific software, including GraphPad Prism and Treestar software’s FlowJo, we are rapidly moving toward achieving our vision.

As always, we welcome your comments and suggestions.  Please comment here, or visit our Support Forum at

New “LA-DOCS” Feature in LabArchives

Our latest release of LabArchives ( includes a powerful new feature that we are calling “LA-Docs”.  In addition to being a very important new function for our users, LA-Docs also is a blueprint for our vision of the future of LabArchives as we continue in our rapid development of this innovative product.

So what is LA-Docs? In a nutshell, it is a new function that enables users of LabArchives to create and edit Microsoft Word, Excel, and PowerPoint documents without ever leaving their Notebooks (you don’t even need a license for Microsoft Office)!  Prior to this, when editing these file types, one needed to save them to their local drive and “re-upload” them to their Notebooks, which required additional steps (as well as remembering to upload them).   Since these document types represent a significant portion of the files used by LabArchives subscribers, this is a major step forward in bringing additional convenience to our customers.    And unlike some other collaborative software, such as Google Docs, your documents never leave the safety of our server (Google keeps copies of all documents that are used in Google Docs).

As enthusiastic as we are about this development, we are even more excited about the potential demonstrated by LA-Docs, and what it means for the future of LabArchives and our vision for the evolution of our product.  Our goal is to make LabArchives the “hub” of the workflow of most scientists by helping to integrate the various software tools that they use with our product so that they can conduct much of their laboratory work from within the “framework” of LabArchives.  Our initial integration with two leading scientific tools, GraphPad Prism and Treestar’s FlowJo, are also indicative of the direction that we are taking.   We plan further enhancements to the integration of these products with LabArchives in the near future;  in the longer term, our goal is to jointly create versions of these and other product on the LabArchives servers, so that licensed users may conduct curve fitting, statistics, flow cytometry analysis, and much more from within their LabArchives Notebooks.

We are currently discussing integration of various bibliographic management software with LabArchives.  We would like to hear from you…our users….as to what products you would like to see integrated with LabArchives.

LabArchives is Officially Released

After more than 18 months and thousands of hours of development effort, we are pleased to announce that LabArchives is now officially available to the public!  For those of you that are new to this Blog, LabArchives ( is an innovative new web-based software service for storing, organizing, sharing, and publishing scientific data (it can also be installed on a local server if desired).

I would like to thank our entire team for their incredible hard work in making this vision into a reality.  Throughout this process, I have been continually amazed at the rapid progress that has been made by our Development and IT teams, and the dedication they have shown in ensuring that we release a powerful yet easy-to-use product with incredible reliability and virtually no downtime….even during development.

I would also like to thank our group of Beta-testers, without whom this release would not be possible.  Their comments and suggestions have truly helped to shape LabArchives into its current form, and will continue to shape it as we implement many new features over the coming months.  LabArchives is truly a customer-driven company, and strongly encourage all of our users to make comments and suggestions, no matter how major or minor they might be.

Finally, I would like to thank our partners at GraphPad Software (makers of Prism) and TreeStar Software (makers of FlowJo) for their early recognition of the potential of LabArchives and for their hard work and efforts in integrating their products with ours.  This collaboration will provide enormous benefits to our mutual users, and we look forward to expanding our interface in the near future.

The NSF and Sharing of Data

One of the most powerful features of LabArchives is the ability to share information…either within your laboratory, with specific collaborators, or with the entire scientific community.  With the click of the mouse, LabArchives will provide you with a URL that will make any selected data available for viewing.  Thus, the recent guidelines by the National Science Foundation (NSF) are of strong interest to LabArchives users, and to the entire scientific community a well.

In guidelines recently published by the NSF entitled Dissemination and Sharing of Research Results, the NSF is requiring their funded investigators to make their data publicly available.  More specifically, they state the following:

“Investigators are expected to share with other researchers, at no more than incremental cost and within a reasonable time, the primary data, samples, physical collections and other supporting materials created or gathered in the course of work under NSF grants.”

Furthermore, any NSF grants submitted after January 17, 2011 must include a proposal on how these data are to be shared:

“Beginning January 18, 2011, proposals submitted to NSF must include a supplementary document of no more than two pages labeled “Data Management Plan”. This supplementary document should describe how the proposal will conform to NSF policy on the dissemination and sharing of research results.”

For those who are using LabArchives, the ability to easily share data is one very simple way that our users may be able to comply with these new rules.  We are also working closely with some archiving sites to make it easy to export these data to 3rd party locations when desired.  Stay tuned for more details.

The NSF  documents explicitly mention that what constitutes an acceptable plan is expected to evolve, as standards, technologies, resources, and community norms change over time.  It is our hope and expectation that LabArchives can help to play a role in this process, which we also believe will be a strong benefit for science as well.

Getting ready for official release and NIH Test

As we near the commercial release of LabArchives as well as testing at the NIH, I am reflecting on the amazing progress made by our Development and IT teams over the last year.  LabArchives is emerging as an extremely easy to use yet powerful tool that we believe will improve the efficiency of many investigators throughout the world.  Our team owes a huge round of “Thanks” to our Beta-testers, many of whom have provided us with excellent suggestions for enhancements (not to mention the location of a few “bugs”), and we are very grateful for their contribution.

We are also excited about two incredible partnerships with other scientific software companies that will benefit many of our mutual customers.  Via the LabArchives API (Applications Program Interface), we have been able to collaborate with our partners so that LabArchives interacts with their software.

Our partner from the inception of LabArchives was GraphPad Software, developers of the very popular Prism software which is a powerful combination of biostatistics, curve fitting (nonlinear regression) and scientific graphing in one comprehensive program ( which is currently used by tens of thousands of scientists throughout the world.  GraphPad has modified Prism and is will be providing a free update to registered users of Version 5 (5.04 for Windows, 5.0d for Mac) which interacts directly with LabArchives via our API.  Users of the latest release of Prism (which should be released within a few weeks) will be able to save Prism files directly to LabArchives; when they are modified, they can be automatically sent back to the same Notebook page (where, of course, all copies are preserved).

Our most recent partner is Treestar Software, makers of the popular and powerful flow cytometry analysis software, FlowJo (, who are currently updating their software to work with LabArchives in a couple of important ways.  In addition to adding the ability to save FlowJo Workspaces, this software is also being enhanced to enable users to automatically query their LabArchives Notebooks and retrieve *.fcs files based on a variety of criteria.

It was a suggestion from the people at Treestar that also led to a new desktop utility that will make this interaction even more powerful.  We are currently testing a program known as “FolderMonitor” that can be installed on any PC and is used to automatically transfer files in specified locations and of the desired types into the LabArchives Notebook.  So, for example, you can install FolderMonitor on the PC that is connected to your flow cytometer and instruct it to automatically send all raw *.fcs files to your Notebook.  There, using our new “Inbox Rules” function, these files can be organized within your Notebook.  As we developed FolderMonitor, we realized that this program can be used for a wide variety of functions…not only for uploading files from automated laboratory instruments.

For those of you who may be attending the the Cytometry Development Workshop (CDW 2010) in Monterey next week, we plan to demonstrate the latest release of LabArchives in interaction with FlowJo.  We look forward to meeting the Treestar / FlowJo development team in person and to brainstorming about additional ways in which we can improve connectivity between our products.

As I mentioned, we are also getting ready for testing of LabArchives at the NIH next month.  We were thrilled when LabArchives was selected as one of only 3 such programs to be considered for adoption by the NIH, and look forward to starting our test (now scheduled for November 16).  We are also grateful to the NIH team who had some specific requirements that we have been able to incorporate into our product.  Perhaps most notably, our team as put together a Desktop version of LabArchives that enables you to work offline, and then “sync” your data back to the server when you are connected.  I will Blog about the test progress once we get started.

Once again, I would like to thank our entire team, our partners at GraphPad and Treestar, our Beta testers, the NIH, and everyone else who has contributed to the development of LabArchives.  We look forward to our commercial release in the next few weeks.


Chance favors the organized lab

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