Presentation on the Eureka Research Workbench being used for an international collaboration

1. Enabling International
Collaboration using the
Eureka Research Workbench
Stuart J. Chalk1, Robert Belford2, Phuc Tran2, and Thanit Pewnim3
(1) Department of Chemistry, University of North Florida, USA
(2) Department of Chemistry, UALR, Little Rock, AR 72204, USA
(3) Department of Chemistry, Silpakorn University, Thailand
schalk@unf.edu
2014 Fall ACS Meeting

2. Lessons Learned
Enabling International
Collaboration using the
Eureka Research Workbench
Stuart J. Chalk1, Robert Belford2, Phuc Tran2, and Thanit Pewnim3
(1) Department of Chemistry, University of North Florida, USA
(2) Department of Chemistry, UALR, Little Rock, AR 72204, USA
(3) Department of Chemistry, Silpakorn University, Thailand
schalk@unf.edu
2014 Fall ACS Meeting

3.  Motivation
 What is Eureka?
 ExptML
 Web Interface
 Collaboration
 Requirements
 Progress
 Feedback
 Lessons Learned
 Future Plans
 Conclusion
Outline
Downloaded from glasbergen.com

4. Motivation
 Science needs to be brought into the 21st century…
at least as far as laboratory notebooks are concerned
 Academics need a cheap (free) equivalent to ELN’s
that are available in industry
 Leverage current web technologies
 Enable global collaboration
 Students need a ‘social media’ app for science

5. Here is some research about urine

6.  Scientists need to move to
digital notebooks…
 ...and record not just the data
but the flow and context
 How science is done
is important for searching,
aggregation, meta-analysis
 We need more than an electronic version of a notebook
 We need a science version of “Second Life” (SciLife?)
Electronic Notebooks

7.  Started in 2006 after getting involved in the
Analytical Information Markup Language (AnIML) project
 Store all research notes/data in a digital format
 Capture the workflow of scientists
 Writing in a lab notebook is equivalent to
“multi-type” blogging in the digital world
 How to capture information? Many data types! (ExptML)
 How to store files “online”? (Fedora-Commons)
 How to access files in the browser? (CakePHP)
 How to represent laboratory resources? (ExptML)
 How to link data together? RDF (in Fedora-Commons)
Eureka Research Workbench (ERW)

8.  A specification (written in XML) that describes different
types of information recorded during the scientific process
(http://exptml.sourceforge.net)
Experiment Markup Language (ExptML)
 Sample
 Solution
 Space
 Specimen
 Substance
 Task
 Template
 Timeline
 User
 Vendor
 Annotation
 Api
 Calculation
 Chemical
 Citation
 Customer
 Data
 Dataset
 Definition
 Element
 Equipment
 Event
 Experiment
 Group
 Message
 Project
 Protocol
 Quote
 Report
 Result

9. Collaboration
 Nonylphenol ethoxylates (NPEs) or octylphenol
ethoxylates (OPEs) in detergents mimic estrogens. These
endocrine disrupting chemicals (EDCs) are problematic to
the environment. Interested in finding out if a microalga,
Chlorella vulgaris is able to biotransform NPEs.*
 Sample collection in Thailand (extracts shipped to UALR)
 Chemical analysis (GC-MS) at UALR
 Research entered in ERW hosted at UNF

10.  Unique identifiers for samples and extracts
 Record
 Sample and extract information
 Procedures for sample collection, extraction, sample
prep, analysis
 Chemicals used
 Analysis data
 All research groups can see all data
Requirements

11. Progress
 Registration of users
 Project, experiment, task creation
 Addition of substances, chemicals, solutions,
equipment
 Upload of
 Data (different formats)
 Citations (research papers, procedures)
 Real time testing demonstrated technical difficulties
 We are still working on resolving these…

12. Feedback
 In Laboratory view, why is ‘vendors’ shown?
 In Notebook view, add ‘Initial procedure’
-> scratchpad (place to doodle, not add to notebook)
 Ability to delete data that is ‘not needed’
-> identify data as ‘junk’
 Difficult to understand the difference between
‘substance’ and ‘chemical’
 View data by research group (not just user)
 View data by project (across multiple research groups)

13. Lessons Learned
 Speak the same language
 Challenge is to capture the many ways
scientists think about science
 Users expect to view data in any file format
 Users just want it to work (‘Apple-like’)
 Develop introductory material for users to evaluate how
they do science – from an informatics perspective
 Provide video (screencast) tutorials
 Provide in-built help
 Design the system to be more flexible to fit users
 Develop a ‘discussion forum’ for users

14. Future Plans
 All of the above 
 Add viewers for all common instrument data types
 Use CakePHP’s Internationalization functions to change
the language of the website interface elements
 Integrate Google translate to automatically convert text
when viewed by a user of another language

15. Conclusion
 International collaboration is hard
 We need to
 speak the same language in science
 get the informatics perspective out of design of interface
 provide functional to translate language
 Provide tools that foster collaboration…
 … that respect issues of privacy and provenance

16.  schalk@unf.edu
 Phone: 904-620-5311
 Skype: stuartchalk
 LinkedIn/Slidehare: https://www.linkedin.com/in/stuchalk
 ORCID: http://orcid.org/0000-0002-0703-7776
 ResearcherID: http://www.researcherid.com/rid/D-8577-2013
Questions?