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ELN articles and other resources

John Trigg — Mon, 30 Jan 2012 15:02:27 +0000

One of the original concepts of this website was to provide a simple portal to published information and opinion about managing laboratory information. Apart from the various accumulated posts, there are a couple of dedicated pages on this website that provide links to other information resources, including a page dedicated to ELN Resources and Articles. John Jones recently kicked off a new discussion in the LIMS Forum on LinkedIn ‘What are some of the key functional requirements of an ELN for Research and for QA/QC?‘ which should attract a lot of good information that will be beneficial to anyone trying to some background to what an ELN is, what it can do, and how to go about getting one. Take a look, and post any additional links to the LinkedIn discussion, or leave a comment here.

9th Forum on Laboratory Informatics

John Trigg — Fri, 18 Nov 2011 15:38:11 +0000

The 9th Forum on Laboratory Informatics was held in San Diego, November 14-16th 2011. The programme embraced a set of three workshops and a two-day session of presentations. Here is a brief review of some of the presentations, with an emphasis on matters relating to laboratory integration.

The opening presentation by Martin Vaderlaan and Eugene Kim (Roche-Genenthech) described approaches taken to integrate LIMS, ELN and Robotics in their laboratories. The presentation served to highlight the benefits of laboratory integration, but emphasised the cost in terms of effort; ten custom interfaces built, requiring three different coding languages. Joe Liscouski (Institute for Laboratory Information) discussed the work of the Institute for Laboratory Automation in developing methodologies and training programmes to address some of the deficiencies in formal education curricula. The ILA now has a membership scheme that offers members the opportunity to collaborate and help define the ILA’s programmes.

Steven Shea (Allergan) described the extension of a commercial Scientific Data Management System to incorporate generic Electronic Lab Notebook functions. The inclusion, management and storage in the SDMS database of MS Office documents (Word/Excel) addressed authoring and worksheet requirements for the laboratory workflow. This presentation identified yet another hybrid approach to address laboratory information management requirements.

IT innovation in the R&D arena was the subject of a presentation by Sanjoy Ray (Merck and Co. Inc.), who described a methodology for driving improvement in IT tools available to R&D workers in Merck. The methodology was derived from the ‘scientific method’, initiated by hypothesis and proceeding via a phased approach towards delivery of a ‘solution’. The presentation addressed a number of cultural and behavioural issues experienced in establishing and deploying the process.

The adoption of standards in the Clinical/Health sector was addressed in two presentations by Sandra Vance (HIMSS) and Daniel Vreeman (Regenstrief Institute). Sandra Vance described the work of HIMSS in advocating and facilitating the adoption of standards, with particular emphasis on clinical laboratories. Of particular interest was the process by which HIMSS engages and encourages vendors to participate and adopt standards through major ‘connectathon’ events in which developers from different vendors sit side-by-side to write and test code to ensure compliance and connectivity.

Daniel Vreeman discussed LOINC® (Logical Observation Identifiers Names and Codes), a standard for the exchange and pooling of results for clinical care, outcomes management, and research. Although most laboratories and clinical services use HL7 to transmit results electronically from their reporting systems to their care systems, the information in these messages are often rendered non-standard due internal inconsistencies of code values. LOINC codes are universal identifiers for laboratory and other clinical observations that provide a common terminology that solves this problem.

My presentation on the Challenges Facing Laboratory Integration is available here:

Laboratory Integration John Trigg

View more presentations from John Trigg

The Leahy Smith America Invents Act

John Trigg — Mon, 03 Oct 2011 10:51:17 +0000

The Leahy Smith America Invents Act was signed by President Obama on 16th September 2011, bringing to culmination a succession of proposed revisions to Patent Law in the US. However, some commentators are expecting the new act to be subjected to revision as a consequence of concerns about potential loopholes. As far as laboratory notebooks are concerned, the switch from first-to-invent to first-to-file would seem to offer some relaxation over the requirements for experiment documentation and witnessing. So, two viewpoints on this: Firstly, in order to comply with first-to-file, the current requirements for the documentation of experiments are quite consistent with good scientific practice and basically make good scientific sense. As such they provide a trustworthy account of inventions, with appropriate authenticity and integrity, sufficient to stand up to adverse scrutiny in a law court. From a sound business and scientific viewpoint, would we really want to back away from this standard of documentation? With science becoming increasingly subject to scrutiny for environmental, health and peer review reasons, forsaking a sound documentation approach doesn’t make sense.

The second viewpoint is that expressed by Colin Sandercock (Perkins Coie LLP) at the recent IQPC ELN conference in Barcelona. This is a brief summary of the points that Colin raised:

(1) Interferences may continue in force for many years and involve inventions made after March 16 2013.

Some of the wording of the new act would potentially lead to interferences and interfering patent actions continuing for many years. More specifically, preserving the right to an interference requires only that the application ‘contains or contained at any time’ a claim to an invention having an effective filing date that occurs before March 16, 2013, or a specific reference (under section 120, 121 0r 365(c) of title 35, United States Code) to any patent or application that contains or contained at any time such a claim.

(2) Derivation proceedings will replace interferences for certain types of inventorship disputes

Derivation requires proof of prior conception and communication to the competing inventor(s). i.e. records may be critical in proving derivation or defending against a derivation claim.

(3) Proof of inventive activities may be needed to remove prior art under exception for joint research activities.

For more detail about the Leahy Smith America Invents Act :

America Invents Act of 2011

Leahy-Smith America Invents Act Implementation

Patent Reform’s ‘Brave New World’ (from Bio-IT World)

IQPC ELN Conference – happy birthday!

John Trigg — Mon, 03 Oct 2011 10:44:49 +0000

The IQPC ELN conference celebrated its 10th birthday in Barcelona last week. As with some ‘application-centric’ conferences, it always seems slightly surprising that we can still find enough to talk about year on year. This year’s conference offered a familiar format of case studies, examples of best practice and topic-based discussion sessions, but there were three particular issues that drew attention. The first of these was that within a number of presentations and panel sessions, there was an unprecedented degree of openness regarding product-related issues. This type of conference usually attracts ‘showcase’ type presentations that illustrate the positive side of ELN deployment. Although the potential benefits of ELNs are generally accepted, a number of speakers made it clear that there are approaches adopted by some vendors regarding customisation and configuration of their products that are not seen as being fully acceptable. These points were raised in a constructive manner on the basis of disappointing experiences in (a) undertaking upgrades on systems with vendor-created customisations, and (b) the creation and management of configurable components such as templates. The time commitment to address these issues is often perceived to be excessive. The second issue was a concern about the lack of modularity in products. The trend has been for ELN products to include more and more functionality, which in turn is driving a level of convergence amongst products in the ELN/LIMS/LES market. This leads to two potential problems; confusion amongst potential customers, and heavyweight products with performance issues. The growing interest in the potential of the ‘cloud’ is somewhat offset by the fog in the marketplace. The other issue was the potential impact of the Leahy Smith America Invents Act on electronic laboratory notebooks. The new act will mean that in 2013 America will change its patent award process from ‘first to invent’ to ‘first to file’. This will seemingly reduce the requirement for a laboratory notebook to be used as evidence in a patent interference, and as such may allow for a less rigid documentation and witnessing process. However, Colin Sandercock (Perkins Coie LLP) raised some important concerns, which are described in a separate post. In summary, there are no grounds for relaxing current practice, since there are loopholes that are likely to allow interferences to continue for many years. Overall, the conference proved to be a good opportunity to catch up on developments, share experiences and concerns, and exploit a new venue with friends, old and new.

Semantic annotation of experimental records

John Trigg — Fri, 30 Sep 2011 11:02:14 +0000

A recent article ‘Where do the ideas come from?‘ I had written for Pharma IQ kicked off a short discussion on a LinkedIn group (LIMS Forum) that included a reference to a paper on ‘Annotating Experimental Records using Ontologies’ by Alexander Garcia, Olga Giraldo, and Leyla Garcia from the University of Arkansas for Medical Sciences, Biomedical Informatics, Arkansas, USA. The paper addresses a growing concern within the laboratory information and knowledge management domain about the ability to efficiently and effectively retrieve records from Electronic Laboratory Notebooks. Their approach was to adopt sematic annotation by combining existing ontologies that support organisation and classification with user generated tagging to generate a three-layer model that relates to the document, the annotation and the experiment. The model allows complex queries based on SPARQL. At present the project is at the prototype stage, but the continuing effort includes plans to release the software to the open source community.

Management Buy-in and User Acceptance in an ELN Project

John Trigg — Tue, 13 Sep 2011 08:00:38 +0000

Management buy-in and user acceptance are two factors regularly identified as critical to the successful outcome of a project. It’s been encouraging to observe, over recent years, that most case studies presented on the deployment of Electronic Laboratory Notebooks (ELNs) that these are two factors that are given more and more consideration in project planning. It goes without saying that management buy-in is essential for an ELN project since the decision to migrate from paper to electronic has far reaching implications beyond the laboratory. Read the full article here.

Yet More on Upgrades (and Replacements)

Gloria Metrick — Fri, 02 Sep 2011 19:44:23 +0000

To explore more of the upgrade portion of the last post, consider these as a fast five things to carefully consider when you’re thinking about whether or not to upgrade versus replacing a system, where these are factors toward replacing it over upgrading it:

1. The system is very old and doesn’t work well.

2. You don’t actually know what all your system is doing.

3. Your system is s data graveyard, a place where the data goes in to die and never to be able to be used for data sharing and knowledge management.

4. The system is a critical one and its technology is out-of-date.

5. Your needs have drastically changed since you purchased it.

Actually, I just copied these points from an older article of mine, but the article is a lot worder than just reading these points in this short form:

http://geometrick.com/n-l-how-to-know-when-upgrade.html

Considerations for laboratory software expansions and upgrades.

Peter Boogaard — Mon, 29 Aug 2011 15:32:00 +0000

Headaches about upgrading your software? Considerations for software expansions and upgrades. Before you decide to rock the boat, several key decision-making steps can help to ensure a smooth and successful upgrade. The last thing to do is to start is a project to change a working enterprise application environment…. Are you ready to sail?

ELNs and Advanced Laboratory Solutions

John Trigg — Thu, 04 Aug 2011 10:23:56 +0000

IQPC’s annual ELN conference, ELNs & Advanced Laboratory Solutions will be celebrating its 10th birthday in Barcelona at the end of September. I would imagine that few of us who attended the first of this series of conferences in London in November 2002 would have thought there would be anything left to say ten years on. But the conversation has changed; in 2002 the questions were what, why and how. In 2011, it’s still the same questions, but the answers are different. Over the ten years, a maturing marketplace and advancing technologies have moved the goalposts somewhat;

The commercial products are more mature, although the marketplace is still very dynamic with merger and acquisition activity, and new players coming on to the scene.
Electronic records can be used as evidence in court.
ELNs really can be used for biology.
The ‘Cloud’ is a remote server farm.
Our vocabulary is being extended to include words such as Semantics and Ontologies.
We need to share data and information across the firewall.
Thin clients become increasingly important.
ELNs can be as portable as paper notebooks.
The need for standards is increasingly recognised.

But there a few things that remain unresolved:

What is the difference between an ELN and a LIMS?
What is a Laboratory Execution System?
How secure is the Cloud?
Will we ever solve the integration problem?

And of course, there are the permanent concerns about best deployment strategies, return on investment, and getting user buy-in.

Click the link for the programme for ELNs & Advanced Laboratory Solutions. The Download Centre contains a number of articles, presentations, podcasts and videos aligned to the ELN event.

The Smart Laboratory: Towards a National ELN

John Trigg — Mon, 01 Aug 2011 10:11:57 +0000

This was a 2 day meeting, as part of the Lab of the Future theme of the EPSRC Dial-a-Molecule Grand Challenge, held in Southampton, UK on 28-29 July.

Dial-a-Molecule is funded by the Engineering and Physical Sciences Research Council (EPSRC), the main UK government agency for funding research and training in engineering and the physical sciences, investing more than £850 million a year in a broad range of subjects – from mathematics to materials science, and from information technology to structural engineering.

Central to Dial-a-Molecule is to be able to predict reaction outcomes, and the availability of high quality data on all reactions carried out is a key enabling resource. A Smart Laboratory must have the collection and use of data at its heart, and a ‘National’ Electronic Laboratory Notebook is a potential means of achieving this objective.

The meeting was attended by a total of 37 representatives of academia, industry and ELN vendors. The programme was a mixture of presentations and workshop sessions. The presentations concentrated on examples of successful deployment of ELNs in industry, the work being undertaken by the Pistoia Alliance to develop standard approaches to data sharing, and ELN initiatives already underway in some academic institutions. In addition, vendors were given the opportunity to present strategies and key features of their products.

The workshop sessions addressed a number of topics
• Why has uptake of ELNs in academia been poor?
• What features would make adoption compelling?
• What other features would we like?
• Any problems that would limit adoption?
• Planning the deployment of an ELN system. Cost estimates.
• Establishing and using a national compound registration system.
• National ELN – beyond synthetic chemistry.
• Defining a common format for data exchange

The outcome of the meeting will be formally reported through appropriate channels in due course, but here are a few personal observations.

• The underlying problems that an ELN can address in industry and academia are very similar, but the context is somewhat different. Primarily it is an issue about intellectual property and the ability to productively manage, use and share IP over its life cycle. The context varies in two ways; firstly, funding and maintaining an ELN in academia presents a different type of challenge. Laboratory productivity will be seen as more of a critical activity in industry (discovery, development, measurement) and will therefore be more readily identified as an area for process improvement. Secondly, laboratories in academia are historically more tolerant of individuality in the choice and use of tools for documenting experiments. The consequence of these two points is that the need for an ELN in academia will require a bottom-up approach with lots of inertia, rather than the top-down that is more common in industry.

• A presentation by Richard Bolton (GlaxoSmithKline) on the progress being made by the Pistoia Alliance ELN Query Service Project in developing a standard approach to sharing ELN data showed considerable consistency with the objectives of the data sharing requirements of the National ELN initiative. If the assumption is that ELN vendors will, in due course, sign up to the Pistoia query standard as it evolves, then a National ELN can take full advantage.

• There are a number of existing deployments of commercial ELNs in academia, as well as non-commercial initiatives (e.g. LabTrove, the Univ. of Southampton project). Adoption is mixed, and a number of speakers from academia highlighted the issue about take-up, e.g. adoption is 90% a ‘user’ issue.

The output from the workshop sessions will be used to refine ideas about, and requirements for a National ELN. Not surprisingly, this output was reasonably consistent with typical requirements from industry-based project dealing with small molecule chemistry. I’ll watch the next steps of this initiative with great interest.

Using SharePoint as an Electronic Laboratory Notebook

John Trigg — Mon, 16 May 2011 14:05:24 +0000

I had the opportunity to interview Tina Spendler, Project Manager for the Novozymes’ ELN project, to get some insight to their choice of Sharepoint as an ELN platform. You can find the interview here. Tina will be giving a presentation on this topic at the 10th Annual ELNs and Advanced Laboratory Solutions Conference in Barcelona, September 26-28th.

Two books on ELNs

John Trigg — Tue, 03 May 2011 13:26:23 +0000

The third edition of “Getting started with an Electronic Laboratory Notebook” has recently been published by Scientific Computing World, and is available from the SCW website.

Also, Labtronics have have published an eBook “ELN and the Paperless Lab” which can be downloaded from the Labtronics website.

Semantics and ELNs

John Trigg — Fri, 29 Apr 2011 10:11:12 +0000

I recently conducted an interview on behalf of Pharma IQ with Jeremy Frey, Professor of Chemistry at the University of Southampton on the subject of semantics and electronic lab notebooks. You can listen to the interview here.

Laboratory information and acronyms

John Trigg — Mon, 14 Mar 2011 11:18:13 +0000

LIMS is Dead! Long live LIMS! – That’s the title of a post on Jeffrey Lee’s JAL Pharmatics website which attracted my attention when it popped up in my RSS Reader. It makes interesting reading, particularly if you substituted your favourite acronym e.g. ELN, SDM, etc. for LIMS. I suspect Jeffrey’s argument (that a specific application represents ‘laboratory information’) holds true, whatever laboratory system you are talking about. In my view, this is a reflection of our classical ‘application-centric’ view of the world. Instead of taking a holistic view of the organisation’s operations, and understanding the relationships between the various functions and workflows, we naturally take the narrower view of the immediate environment and try to solve whatever problems show up there. But we tend to identify, and try to resolve the ‘problems’ in the context of the application. This in turn muddies the water when it comes to defining a LIMS or ELN, since the terms become inherently ambiguous. One man’s LIMS may be another man’s ELN! – as if we didn’t have enough problems with achieving a common vocabulary already.

Unfortunately, taking the wider view tends to be a theoretical exercise, since the platform and the set of tools that is required to satisfy the broader set of requirements doesn’t really exist, especially if you are looking at a best-of-breed approach. In fairness to some vendors, this approach does exist to some extent within an application (LIMS and ELNs); you but the generic capability, and plug-in additional functions to address specific requirements, but there are usually boundaries between the applications that present an integration challenge that will absorb a number of resources to resolve, without necessarily achieving desired quality and efficiency gains.

W.E. Deming’s point that the latest new gadget will not fix your quality challenges, may equally apply to the latest new application.

eOrganizedWorld Online Information Management Newsletter

Charlie Sodano — Mon, 14 Mar 2011 10:17:19 +0000

All thumbs
Do you ever get frustrated because your mind is moving much faster than you can work with the devices used to interact with your computer? I never really learned to type on a keyboard very well, but did buy some software years ago to practice with and got decent. As time went by my fingers moved away from the “home keys” and now float where ever they are needed. It’s not as bad as it sounds. At least I use both hands!

I did give Dragon Naturally Speaking software a shot. Wasn’t that bad to get started, but since my composing style involves many rewrites, edits and redos, it was too clunky for me to use routinely. And there were days when I mumbled more than usual. Dragon could not translate my mumbles very well. I always thought it would be an excellent tool for medical writers or other people whose prose is more predictable..

Other than typing letters and symbols, do you use any of the other keys to help productivity? Let’s get back to that in a sec. What kind of mouse do you like to use? I find that people are very fussy about their preferences; track ball, joy stick, touch pad, eraser stick, and click and scroll mice to name a few. I’ve found that none of them are as good or fast as my finger navigation. But double clicking or right clicking your finger is a challenge for most devices. The iPad is not a device that is good for most business processes, although I’m sure there are a bunch of people out there who are “making” it work.

I’ve been using laptops for the past 20 years or so and when traveling I have had “mouse” failure at least twice. The first time was traumatic. It took me forever to do things, but by trial and error I did figure how to do some “mouse things” via my keyboard. When I got home, I did a little more research and discovered that it is possible to go almost completely “mouseless”. There are actually more key commands out there than you would ever want or need. I tried a bunch of them and eventually settled on several that I continue to use today in concert with my mouse. Like touching finger to the screen, there are some things that are way easier to do with a keystroke.

These are my favorites, (sorry to the MAC users), starting with the ones I use the most. There are many other keyboard shortcuts, but unless you hate mice (or rats) they don’t add much,
Windows logo key +E = Open computer Explorer

Windows logo key +M = Minimize all windows

F12 opens the Save as window in Microsoft Office apps.

F5 Refreshes current browser page, frame, or tab.

Ctrl + A = Select all text.

Ctrl + X = Cut selected item.

Ctrl + C = Copy selected item.

Ctrl + V = Paste

Alt + F4 Closes Current open program.

Shift + F3 will change the text in Microsoft Word from upper to lower case or a capital letter at the beginning of every word. (This is great after you discover your been typing away with the CapsLk on).

F5 Starts a slideshow in PowerPoint.

B displays a black screen during a PowerPoint presentation (great for getting your audience’s attention!). Hit B again to resume. Try using W if you are a bright person.

I hope that I pressed some of your buttons.

What’s new?

Content Management.

Workshare released Workshare Point, software which enables users to retrieve and file content to Microsoft SharePoint without leaving Microsoft Office applications. The Workshare Point solution provides a tight integration between the Office products and SharePoint, so users may access SharePoint quickly and easily from within the familiar Office and Outlook navigation interfaces.

OpenText Corporation announced portal solutions that enable customers to create best in class social-, content- and customer-centric sites. The new OpenText Portal software includes a set of powerful portlets that allow users to easily mashup content from Microsoft SharePoint, OpenText ECM Suite and many other sources into a single, highly flexible and personalized interface, for intranet, extranet, or customer-facing websites.
Alfresco Enterprise 3.4 isthat platform with open standards like CMIS, JSR-168 and RESTful API’s manages content and expose repository functionality inside of social business systems.Alfresco’s refreshed Share interface for collaboration and document management now includes status updates (similar to Facebook and Twitter), content activity streams and enhanced search capabilities to make content easier to find.

SpringCM, unveiled new cloud enterprise content management platform.The new cloud enterprise content management platform features enhanced e-forms and metadata functionality that enable easier and faster deployment of SpringCM for process-automation, workflow and document-management applications.