Integrating Jmol/JSpecView into the Eureka Research Workbench

Israel Hurst, Matthew Morse, and Stuart J. Chalk

Department of Chemistry

University of North Florida

schalk@unf.edu

2014 Fall ACS Meeting

Motivation

What is Eureka?

What is JSmol?

What is JSpecView?

Integrating Jsmol into Eureka

Using JSpecView

Using JCAMP-MOL files

Generating JCAMP-MOL files

Future Plans

Conclusion

Outline

Motivation

All Electronic Laboratory Notebooks need to display

Molecular structures

Instrument Data

Jmol (a Java Applet) has be the standard, open source molecular viewer for the last 20 years

Jmol now incorporates JSpecView (also Java)

Jsmol is the javascript version of Jmol -> HTML 5

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

What is Jmol?

Java application, applet and viewer for chemical structures in 3D (http://www.jmol.org/)

Developer Dr. Robert Hansen (+ many others)

Open source, cross platform since 2001

Display of over 30 chemical structure formats

Animations, vibrations, surfaces, orbitals

Support for unit cell and symmetry operations

Measurements – distance, angle, torsion angle

Support for RasMol/Chime scripting language

JavaScript support library (Jmol.js)

Exports to jpg, png, gif, ppm, pdf, …

What is JSpecView?

Java based application and applet (for web viewing)

Developer Dr. Robert Lancashire

Licensed version 2001, open source since 2006

Display/print JCAMP-DX, AnIML, and CMLspec files

Highlighting, zooming, coordinate data

Absorbance/Transmittance conversion (UV/Vis and IR)

Predict the colour of a Visible spectrum

Integrate H NMR spectra

Java scripting and Live Connect support

Export JCAMP-DX, AnIML, CML, JPG, PNG or SVG

Integrating Jsmol into Eureka

Eureka is built using the CakePHP framework

CakePHP uses the Model-View-Controller software architecture paradigm

Model – interaction with database/datasource

View – display of web page

Controller – logic to take data from model to view

Jsmol best implemented as a plugin

Jsmol has ‘datasource’ – file that is to be displayed

CakePHP MVC

Views are made up of base code and ‘elements’

Elements are reusable code snippets that can be displayed on any page

For optimum functionality display Jsmol via an element

Jsmol CakePHP Plugin

Architecture of plugin the same as the main CakePHPapplication

Issues to overcome

Jsmol likes files in a certain location relative to the main javascript file (Jsmol.min.js)

CakePHP does not allow access to non-PHP files in folders containing view files

How to integrate?

Jsmol CakePHP Plugin

Convoluted scheme finally allowed integration

File in plugin ‘webroot’ folder contains Jsmol code

This file is called by view file via an iframe

Display parameters are sent via GET variables on iframe URL and retrieved by javascript

Element file uses CakePHP ‘requestAction’ function to display view file code

echo $this->element('Jmol.molecule’,array(…));

Future Plans

Add more GUI options to control look and feel of JSmol

Add ability to link spectral features to molecule

Add other molecular and spectral viewers to Eureka so users can customize the interface

Conclusion

Building out Eureka with ‘plugin’ features is a great way to enhance the usefulness of the system

Providing a tutorial on how to build functionality into Eureka will encourage users to add what they need for their research

Move Eureka code development to GitHub

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?