electronic laboratory notebook in the graduate level...

Electronic Laboratory Notebook in the Graduate Level Laboratory Informatics

Program

Mahesh Merchant, Paresh Sanghani*, Sonal Sanghani*

Mahesh Merchant

Indiana University School of Informatics

[email protected]

* Department of Biochemistry and Molecular Biology

• Five master’s degrees:– Bioinformatics– Chemical Informatics/Laboratory

Informatics– Health Informatics– Human Computer Interaction– Media Arts & Sciences

• Now offering Ph.D. in Informatics• Masters in Biochemistry and

Molecular Biology

Graduate Programs

• Laboratory Information Management Systems (LIMS)

• Electronic Laboratory Notebooks (ELNs)

• Data Visualization• In-house Databases• Enterprise Resource Planning, SAP

Data Integration

Data consumers

Data sourcesLab instrumentation Office

applications

LIMSVisualizationand analytics

softwareE-Notebooks Discovery

Databases

Print and file data

The integration challenge

©2004 Waters Corporation

• Two commercial LIMS (Labware and LabVantage)

• Currently, one commercial ELN (LabTrack)• Currently, one Enterprise Content

Management System (Cerity) • Data Visualization Software (Spotfire)• Chromatography Data System

(PerkinElmer)

Software at Indiana University

• ELNs are taught in the Scientific Data Management Class as part of the Laboratory Informatics curriculum

• Two student projects involving Gene Expression using microarrays and the Protein Data Bank are highlighted in today’s presentation

• Students use an Enterprise Content Management System (ECMS) in conjunction with the ELN

ELN in a Classroom

ELN - Gene Expression Project

ELN – Metadata Definition

ELN – Data Visualization

ELN – Conclusions

ECMS – Project Layout

ECMS – Metadata

ELN – Protein Data Bank Project

ELN – Questions to be addressed

ELN – Project Outline

ELN – PDB File Parser

ELN – Database

ELN – Data Visualization

ELN – Daily Log of Problems Encountered

ELN – Database Queries

ELN – Results and Discussion

ELN – Conclusions

ELN – Methods in Cell Biology

• This course involves discussions and hands on experimentation in basic and advanced cell biology techniques

• Students are required to keep a laboratory notebook describing the objective, methods, results and conclusions of their experiments

• Homework questions associated with each experiment are answered in the laboratory notebook

ELN – Challenges for the Cell Biology Class

• This course involves multiple instructors with laboratories located in different buildings

• The handouts for the laboratories are in different formats, e.g. PowerPoint Slides, Reference Articles, Laboratory Procedures

• Analysis of data is performed using a variety of software packages

• Resources

ELN – Laboratory Handouts and Analysis

ELN – Adding Comments with a Tablet PC using Ink Window

ELN – Laboratory Comments

ELN – Future Directions

• Integration with SDMS and other software

• Open architecture to allow products from multiple vendors to communicate with each other

• Use of Tablet PCs in the Laboratory

Integrating SDMS into your overall business process

Data consumers

Data sourcesOffice

applications

Waters NuGenesis SDMS

View

Extract

LimsVisualizationand analytics

softwareE-notebooks

Discoveryand clinicalDatabases

Lab instrumentation


eLab Notebook View of SDMS Data

NMR

HPLC


SDMS Data from eLab Notebook

SDMS Vision Data Source

Select Data to View


Data is selected then sent to the eLab Notebook

Acknowledgements• Students from my Class

• Waters Corporation

• Agilent Technologies (Scientific Software Inc. has been purchased by Agilent)

• Spotfire

• LabTrack

• PerkinElmer

• Dr. Paresh Sanghani

• Dr. Sonal Sanghani

electronic laboratory notebook in the graduate level...

Documents