ACS 248th Paper 67 Eureka Collaboration

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, [email protected]

2014 Fall ACS Meeting

Lessons LearnedEnabling InternationalCollaboration using the

Eureka Research WorkbenchStuart 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, [email protected]

2014 Fall ACS Meeting

Motivation What is Eureka? ExptML Web Interface Collaboration Requirements Progress Feedback Lessons Learned Future Plans Conclusion

Outline

Downloaded from glasbergen.com

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

Here is some research about urine

Scientists need to move todigital notebooks…

...and record not just the databut the flow and context

How science is doneis 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

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)

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

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

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

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…

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)

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

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

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

[email protected] 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?