Posts Tagged 'LabArchives'



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 http://dx.doi.org or http://crossref.org.

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 www.labarchives.com.

New “LA-DOCS” Feature in LabArchives

Our latest release of LabArchives (www.labarchives.com) 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.

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 (www.graphpad.com) 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 (www.flowjo.com), 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.

LabArchives at Experimental Biology (FASEB)

We recently returned from our first public exhibition of LabArchives at the Experimental Biology meetings in Anaheim.  Because we are still in “Beta”, our objectives in this meeting were to obtain valuable feedback from the scientific community, as well as to sign up some additional testers;  by this measure, our exhibit was a resounding success!

It had been nearly 20 years since I have attended a FASEB meeting;  the size seemed to have decreased substantially (or perhaps my memory is in question). There were roughly 12,000 scientific attendees, and I recall numbers in excess of 20,000 at one time.  Of course, I am sure that this meeting was significantly reduced in size due to the eruption of the volcano in Iceland which greatly disrupted worldwide travel.  In fact, we spoke to very few people from outside of the US at this meeting.

In spite of the lower attendance, we were able to speak with (as well as demonstrate LabArchives) to over 50 investigators, virtually all of whom shared the same problem of organization of data in the laboratory.  Every one of our visitors still maintain paper notebooks, and all vocalized the problems of retrieving data…especially when someone had left the lab.  One individual with whom I spoke discussed looking for the data of a Post-Doc that had left the lab.  When their notebook was found, it simply contained a pile of X-Ray films that had been stuck into the notebook.  In short, over a year’s work was effectively lost.

This theme, as well as the issue of laboratory staff failing to keep a good notebook, as well as that of collaboration with individuals throughout the world, were frequently repeated.  Every person who looked at LabArchives agreed that it would help solve these issues.  The critical point, of course, will be to get their teams to implement LabArchives.  A number of our visitors have agreed to become Beta-testers of LabArchives, and we are now beginning to see a rapid increase in usage from both small and large laboratories.

In addition to signing up a number of users, we were able to receive some important feedback from visitors to our booth.  When we started development of LabArchives as a web-based tool, we designed it in such a way that it would be easily adapted to running in “locally hosted” environment.  In visiting with users at FASEB, we quickly learned that the demand for a local version would be almost as strong as for the web-based product.  This demand stems both from users that have very large files (our web product limits individual files to 50 MB), as well as from security issues or policies.  Based on this feedback, we are expediting our local-hosted development, and are currently seeking a few additional testers for this version.  Please contact us if you would be interested in LabArchives installed on your own servers.

In the few weeks since FASEB, we have made a number of significant enhancement to LabArchives, based both on our meetings as well as feedback from our users.  If you haven’t had an opportunity, please visit our website at http://www.labarchives.com, and/or contact us if you would like a demonstration or to become a Beta-tester.  We hope to have our commercial release early this summer.

“Chance favors the organized lab”

Welcome to the premier blog entry for LabArchives, the new web-based software to enable investigators to organize, track, retrieve, and selectively publish laboratory data.  We are currently in beta-test, and plan for a full commercial release in the next 2-3 months.

I would like to begin with apologies to Louis Pasteur, for our slight modification of his famous quote: “Dans les champs de l’observation le hasard ne favorise que les esprits préparés” which is generally translated as “In the field of observation, chance favors the prepared mind”.  This is as true today as it was in 1854 when Pasteur stated this at the University of Lille.  Just as true…perhaps even more so…is that organization and management of laboratory data, which is even more extensive today , is critical to the success of every investigator.  It was with this concept in mind that the development of LabArchives began last year.

In this blog entry, I would like to introduce the LabArchives company, and to tell you a little more about our team’s background, the concept behind our development of LabArchives, and what we view for the future.

The company is headed up by myself, Earl Beutler, and Kirk Schneider, our Chief Technology Officer.  Kirk and I have a long history in developing successful and innovative software products for the scientific community, including Research Information Systems (now owned by Thomson-Reuters), which created Reference Manager, the first bibliographic management software product, and Reference Update, which was the first successful “current awareness” service for biomedical investigators.  In 2001, we co-founded RefWorks (now owned by ProQuest), which created the first web-based bibliographic software product, now with over 1,000,000 users at over 1,000 academic institutions throughout the world.

While working with scientists over the past 30 years, a period during which the use of computers and the Internet has exploded in the scientific community (not to mention the rest of the world), and the amount of data and information has increased by an order of magnitude, the maintenance and organization of these data has remained strikingly archaic.  In fact, I remember speaking to one well-known scientist about how he maintained all of his images.  He showed me how he took pictures with a digital camera, printed them, and then glued them into a paper notebook!  This struck me as such an anachronism and with it began the seed of LabArchives.  More than just an “Electronic Laboratory Notebook” (or ELN as these have come to be known), LabArchives provides a platform for sharing, collaborating, and publishing selected results.

While there a number of commercial applications, most are needless complicated, expensive, and targeted at the commercial marketplace.  Furthermore, most are desktop bound, and thus limit the ability to collaborate and publish, an essential component of LabArchives.

So we welcome you to our blog, and invite you to become a beta-tester and, subsequently, a subscriber to LabArchives.  Please visit our web page at www.LabArchives.com to set up your account and begin using our software today.



LabArchives


Chance favors the organized lab

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