Burkhard's AnIML Blog

AnIML at SLAS 2012

Mon, 30 Jan 2012 11:00:31 -0500

For those of you attending SLAS 2012 in San Diego next week, I've put together a collection of activities around the emerging AnIML standard at the conference. Please leave a comment if I missed anything.

This is the first joint SLAS conference after the merger of SBS and ALA.

Saturday Short Courses

Applied IT for the Laboratory
Burkhard Schaefer, BSSN Software
Link to Abstract

Sunday Short Courses

Introduction to Laboratory Automation
Steve Hamilton, Sanitas Consulting
Gary Kramer, NIST
Jay Gill, Brystol-Meyers Squibb
Link to Abstract

XML for the Laboratory
Burkhard Schaefer, BSSN Software
Link to Abstract

Technical Program

Cloud-based Collaboration and Long-Term Archiving Using the AnIML Standard
Wednesday, 2:00 pm - 2:30pm, Informatics Track, Room 1A

This talk discusses using the emerging ASTM AnIML data standard for cloud-based collaboration and archiving of laboratory data. Using AnIML, we implemented a system which allows vendor- and device-independent storage and sharing of laboratory raw and result data in the cloud.

The first part of the presentation focuses on collaboration between cross-organizational teams and sharing of result information using the cloud. A hosted application provides interactive access to analytical results using a web-browser, allowing end-users from different groups to access and share data seamlessly without the need for local software installation. Usage of the AnIML standard has allowed us to manage data from different instruments without requiring access to the original vendor software.

The second part describes how the same is used to archive laboratory data for the long term. The presentation concludes with a discussion of the total cost of ownership and the lessons learned.

Late Night with LRIG

Late Night with LRIG is an interactive forum to discuss and learn about the latest innovations in technology products and services impacting laboratory automation and screening. We'll be showcasing our new Contract Research Manager solution.

Streamlining Contract Research and Contract Laboratory Integration
Monday, 7:00 pm - 9:00 pm, Marriott Hotel, San Diego Ballroom A

Special Interest Group Meetings

SLAS is continuing the tradition of special interest groups (SIGs) from the SBS days. The meetings take place over lunch on Wednesday. Unfortunately, they all take place at the same time, so you'll have to make a choice.

Standards SIG Meeting
lead by Gary Kramer, NIST
with an AnIML talk by Gary

Informatics SIG Meeting
lead by Jay Gill, Brystol-Myers Squibb
with an AnIML talk by Burkhard

Exhibition

Yes, BSSN Software is exhibiting, too. Find us at booth 245, located just next to Innovation AveNew. We have a nice AnIML show case set up, so you can see the standard in action for yourself. This year, we're launching Contract Research Manager, a tool to make it easier to integrate with CROs and contract labs. We have a new version of Seahorse Scienfitic Workbench, including workflow management and many new instrument drivers for analytical equipment and bioprocessing.

Twitter Coverage

Follow @BSSN_Software or @BurkhardS. Also, there's the #slas2012 hashtag.

Five new GC detector techniques for AnIML

Mon, 24 Oct 2011 15:57:21 -0400

Over the past few weeks, Gary Kramer and I have worked on creating five new AnIML technique definitions for the most common GC detectors. We've chosen them based on feedback from the AnIML committee members. These new technique definitions allow us to represent GC experiments more completely in AnIML.

If you use Seahorse Scientific Workbench, you can view them using the integrated Technique Browser. We have pushed out the update to the Technique Catalog this afternoon. You can also view the technique documentation on the web at the following locations:

Electron Capture Detector
https://apps.bssn-software.de/techniquedocs/out/ecd-trace/

Flame Ionization Detector
https://apps.bssn-software.de/techniquedocs/out/fid-trace/

Flame Photometric Detector
https://apps.bssn-software.de/techniquedocs/out/fpd-trace/

Nitrogen-Phosphorous Detector
https://apps.bssn-software.de/techniquedocs/out/npd-trace/

Thermal Conductivity Detector
https://apps.bssn-software.de/techniquedocs/out/tcd-trace/

The documentation automatically updates as the technique definitions evolve.

We're now looking for feedback on these. So if you're into GC, we'd appreciate if you could take the time to look at these and post your feedback below. You can also contact us privately, if you prefer.

AnIML Activities at Pittcon 2011

Thu, 10 Mar 2011 19:00:00 -0500

As we're getting ready for Pittcon in Atlanta next week, I'm picking up on my tradition to collect the different AnIML-related activities at the conference into a blog post. So if you're interested in AnIML, SEDD or data standards in general, you're encouraged to attend. Don't miss our AnIML-in-Action Showcase in the exhibit area.

Sunday

Long-Term Archiving of Laboratory Data (Short Course)
Half-day short course about storing laboratory data for the long term. Focuses on the use of XML and AnIML for archiving purposes.
Burkhard Schaefer, BSSN Software
8:30 AM - 12:30 PM, see the short course desk to register ($225-325)

Implementing AnIML 1.0
An entire session devoted to AnIML, the progress of the standard, and the collaboration with EPA SEDD.
1:00 PM - 4:00 PM, Room 408

Seeing the AnIML from 10000 Meters
Burkhard Schaefer, BSSN Software
What AnIML is Not
Gary W. Kramer, NIST
AnIML Technique Definition document for Chromatography
Maren Fiege, Waters
Crosswalking AnIML with Legacy Data Formats
Stuart J. Chalk, University of North Florida
U.S. EPA's Staged Electronic Data Delivery Format
Anand Mudambi, U.S. EPA
Implementing AnIML with SEDD Stage Four
Joseph F. Solsky, U.S. Army Corps of Engineers,
presented by Anand Mudambi

Monday-Thursday

AnIML-in-Action Showcase by BSSN Software (Exhibition Area)
BSSN Software has set up a showcase of real-life AnIML applications. If you'd like to see AnIML running for yourself, stop by at booth 5155 and take a tour. We're showing our solutions to integrate AnIML into laboratory processes. Instrument and software vendors can learn about our OEM offerings to quickly bring AnIML functionality to their products. You can also see the integration of AnIML and SEDD in action.
Booth 5155

Tuesday

How can I share my data with others? (Conferee Networking Session)
In this networking session, conferees are invited to exchange opinions around standardized data sharing and result delivery. The main topic will be the use of AnIML in the next stage of the U.S. EPA's Staged Electronic Data Deliverable (SEDD). Anand Mudambi and I will kick off the session with a quick summary of the integration of SEDD and AnIML to get the discussion rolling. Please come and share your thoughs.
Anand Mudambi (US EPA), Joseph Solsky (USACE), Burkhard Schaefer (BSSN Software), Gary Kramer (NIST)
8:30 AM - 10:30 AM, Room 216B

Please leave a comment if you are aware of other Pittcon activities that should be on this list. I will add them then.

JALA is now indexed by Thomson Reuters' Journal Citation Reports

Tue, 11 Jan 2011 10:57:00 -0500

The Journal for Laboratory Automation (JALA) is an official journal of the Society for Laboratory Automation and Screening (SLAS). According to Editor-in-Chief Dean Ho, JALA was accepted for indexing by Thomson Reuters’ Journal Citation Reports®, including Thomson Reuter’s Science Citation Index Expanded (also known as SciSearch), Journal Citation Reports/Science Edition, Biological Abstracts and BIOSIS Previews.

JALA manuscript abstracts are already indexed by Analytical Abstracts, Chemical Abstracts (CAS+), CINAHL, Compendex, EMBASE / Excerpta Medica, Google Scholar, Inspec, Proquest CSA Technology Research Database, SciFinder, Scirus, and Scopus. [Source: SLAS]

Why is this additional indexing service important? It means JALA will have an impact factor. A journal's impact factor indicates the average number of citations to articles published in a journal. Many regard this as a measure for the relevance of the journal within its field. One could compare it to PageRank, the algorithm Google uses to measure the relevance of a web page. Higher impact factors make it easier for a journal to attract authors and manuscript submissions. JALA was accepted with the 2009 volume. During 2011, the service will track citations to articles published in 2009 and 2010. JALA’s first impact factor will be announced in June of 2012. If you are looking to publish a paper on a lab automation-related topic, take a look at JALA's online archive and author information.

Disclaimer: I'm serving on JALA's editorial board.

AnIML Activities at Pittcon 2010

Fri, 26 Feb 2010 01:32:00 -0500

For those of you who are interested in AnIML and data standardization, here's a list of AnIML-related activities at this year's Pittcon.

Monday

AnIML: An Analytical Data Standard for the Lab and the Enterprise
An entire session devoted to the use and implementation of AnIML.
8:00 AM - 12:30 PM, Room 205C, Session 370

How Can Instrument Vendors Report Raw Data in a Uniform Open Non-proprietary Standard Format (XML)?
Conferee networking session Anand Mudambi (US EPA), Joseph Solsky (US ACE), John Nebelsick (US EPA), Gary Kramer (NIST), Burkhard Schaefer (BSSN Software)
5:00 PM - 7:00 PM, Room 311H

Tuesday

ASTM E13.15 Annual Business Meeting
10:00 AM - 11:00 AM, Room W230C

ASTM E13.15.1 AnIML Task Group Meeting
3:00 PM to 5:00 PM, Room W230C

XML, Metadata, and Markup Languages for Chemists (Short Course)
One-day short course about the basics of XML, identifying metadata, writing XML for your applications, and markup languages like AnIML.
Stuart Chalk, University of North Florida

Wednesday

Long-Term Archival of Laboratory Data (Short Course)
Half-day short course about storing laboratory data for the long term. Covers the use of XML and AnIML for archiving purposes.
Burkhard Schaefer, BSSN Software

Thursday

Emerging IT for the Laboratory (Short Course)
One-day short course giving an overview of emerging technologies in laboratory informatics. Covers AnIML as a format for data exchange.
Burkhard Schaefer, BSSN Software

If you aware of additional activities that should be on this list, please leave a comment below.

Original AnIML paper in JALA now available as Open Access content

Fri, 29 Jan 2010 23:58:00 -0500

Having taken my seat on the editorial board of JALA, the Journal of the Association for Laboratory Automation, I have learned that Elsevier has made access to many of its articles available as open access content. This means that the original AnIML paper I published in 2004 is now openly available to everybody. Today's AnIML version is slightly different to the one described in the paper. However, it presents a nice overview.

The full article citation is:

Documenting laboratory workflows using the Analytical Information Markup Language
Journal of the Association for Laboratory Automation, Volume 9, Issue 6, Pages 375-381 B. Schaefer, D. Poetz, G. Kramer doi:10.1016/j.jala.2004.10.003

To get it, go to the DOI, then click "JALA" (not ScienceDirect). Enjoy.

AnIML Activities at ALA LabAutomation 2010

Mon, 18 Jan 2010 14:42:00 -0500

Are you attending the LabAutomation 2010 conference in sunny Palm Springs next week? There are a lot of opportunities to learn about AnIML. I have put together a list of AnIML-related activities. I'd especially like to point out the AnIML Birds-of-a-Feather Session on Tuesday evening. This will be a nice opportunity to meet the AnIML community. Please stop by and say hello.

If you are aware of other related activities, please leave a comment below and I will add them.

Short Courses on Saturday and Sunday

XML in the Laboratory Short Course, Burkhard Schaefer
Applied IT for the Laboratory, Burkhard Schaefer

Monday

Poster Presentation
A Step by Step Guide: Creating an AnIML File Writer for an Instrument (MP05)
Dennis Backhaus, Burkhard Schaefer, Reinhold Schaefer, Gary Kramer

Late night with LRIG, a rapid-fire innovation session
Open Data Management and Archiving Platform Based on the AnIML Data Standard
BSSN Software
7:00 pm – 9:00 pm Mojave Learning Center, Renaissance Palm Springs Hotel

Tuesday

AnIML Birds-of-a-feather meeting
Hosted by Burkhard Schaefer (BSSN Software) and Gary Kramer, (NIST)
6:15 pm – 7:15 pm
Room Chino B, Renaissance Palm Springs Hotel

Wednesday

Podium Presentation
A standards-based method for processing and archival of multi-technique experiment data
Burkhard Schaefer 9:30 am – 10:00 am Mojave Learning Center, Renaissance Palm Springs Hotel

Exhibition

BSSN Software – booth 592A in Innovation AveNEW

Download this as a handy printable PDF flyer. See you in Palm Springs!

ALA chooses BSSN Software to be part of Innovation AveNEW at LabAutomation 2010

Tue, 24 Nov 2009 12:00:00 -0500

A judging panel of the Association for Laboratory Automation (ALA) has chosen BSSN Software to be part of its Innovation AveNEW program at the LabAutomation 2010 conference in January 2010.

To quote from the press release: The Association for Laboratory Automation (ALA), a multi-disciplinary, non-profit scientific society serving diverse industries and technology sectors, has selected eight elite start-up companies from around the world for its fourth annual Innovation AveNEW program at LabAutomation2010, January 23-27, 2010, in Palm Springs, CA, USA. The mission for Innovation AveNEW is to offer start-up, entrepreneurial companies operating within the laboratory automation and technology field a venue for positive, collaborative interaction and exposure for their product and/or service concept. Innovation AveNEW will be presented in a specially designated area on the LabAutomation2010 exhibit floor.

We'll be located at booth 592A in the Innovation AveNEW exhibit area. Meet our team and experience our AnIML technology first hand. Check our special page for LabAutomation and find out what else we're doing at the conference. We're looking forward to meeting you in sunny Palm Springs.