The Integrated Lab

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.

Peace in our Time? R&D and the IT Department

John Trigg — Fri, 30 Dec 2011 10:41:08 +0000

The latest article in my column on the Pharma IQ site has just been published. You can read the full article here: Peace in our Time? R&D and the IT Department

The intro:

One of the consequences of the increasing convergence of science and technology is the nature of the relationship between R&D and IT. As scientists increasingly depend on information technology as an integral component of laboratory work, they become increasingly dependent on the IT infrastructure and IT resources. It hasn’t always been like this; in the days when most laboratory computers were basically standalone devices, dedicated to specific data acquisition and/or data processing tasks, life was a lot simpler; scientists could tinker with their systems whilst IT managed the mainframes. But inevitably, as the demand grew to connect things together and transfer data from one system to another, it became necessary to start a relationship with the IT Department. And so began a courtship that, to all outward appearances, was not made in heaven…………..

Just as the article was published, I came across a contribution on the ComputerWorld website entitled: IT managers are aloof, insular, says psychologist. The article was making a very different point,with which I don’t agree; I’ve worked with a number of IT Managers who are far from being aloof and insular. (The article generated a fair amount of comment, probably from outraged IT Managers!). So, in defence of IT Managers, and to reinforce my point in my article, the IT Department has specific responsibilities that demand a good deal of care and caution in order to maintain a robust and reliable infrastructure. The IT ‘culture’ is therefore quite different to an R&D environment where innovation and creativity are key qualities, and it is this difference in cultures, not aloofness and insularity that can cause some of the tension between R&D and IT.

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

Membership in the Institute for Laboratory Automation…

John Trigg — Thu, 10 Nov 2011 16:16:07 +0000

The Institute for Laboratory Automation has announced a membership scheme.

Lab automation technologies can transform lab work. Before we can reap those benefits we have to transform the way people approach lab automation. That is what this organization is about: helping people learn how to plan, implement, evaluate and use the products & technologies available to them.

Laboratory automation has become a cooperative process between scientists and those specializing in the implementation of automation systems. This includes scientists, information technology specialists, vendors, developers, robotics’ specialist, etc. As an organization, the membership work of the ILA is to bring these people together so that they can:

understand each others perspectives,
devise methodologies to get work done,
discuss products and their application, and
develop the tools (education, methodologies, etc.) needed to turn lab automation into a successful pursuit.

To that end, we believe:

that those working in the field need to form a community to develop and improve the practice of applying automation and information/computing technologies to lab and scientific work.
In addition we see the establishment of Laboratory Automation Engineering as a field of work, study, and research, as a necessary goal.

For more information visit: http://www.institutelabauto.org/membership/membershp.html

To join: http://instituteforlaboratoryautomation.camp8.org/

Is the cloud ready to cross the chasm in R&D?

Peter Boogaard — Sun, 30 Oct 2011 21:35:15 +0000

Is the cloud ready to cross the chasm in R&D?

The latest weather forecasts predict more clouds on the horizon in R&D. What is your answer? Leaving our umbrella home? IndustrialLabAutomation, interviewed industry experts about their view deploying cloud services. The article includes a handy cloud summary table. Read more and get your latest weather forecast…

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.

GSK + McLaren

John Trigg — Mon, 19 Sep 2011 08:22:43 +0000

One of the more intriguing recent announcements is the 5yr partnership between GlaxoSmithKline and Formula 1 racing Team McLaren. There’s plenty of speculation about the rationale behind the deal, and who will get the most benefit, but there does seem to be an emphasis on GSK leveraging McLaren’s expertise in real time monitoring and control (of 200+ mph racing cars) for pharmaceutical manufacturing and R&D. Not an obvious connection, admittedly, but its good to see organisations looking outside their normal industry sectors for best of breed expertise. I wonder whether it would catch on?

LIMSource Purchased by Technology Networks

Gloria Metrick — Tue, 13 Sep 2011 11:34:11 +0000

LIMSource, the oldest on-line directory of LIMS, has been purchased by Technology Networks. Read more at the LIMSource home page:

http://limsource.com/home.html

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?

The Challenges Facing Laboratory Integration

John Trigg — Fri, 12 Aug 2011 08:35:45 +0000

I will be giving a presentation on ‘Overcoming the Challenges Facing Laboratory Integration’ at the forthcoming 9th Forum on Laboratory Informatics, to be held in San Diego, Nov 14-16th. As part of the lead up to the meeting, I was recently interviewed on this topic, and the podcast is available on the conference website.

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.