Electronic Laboratory Notebook in the Graduate Level Laboratory Informatics Program Mahesh Merchant, Paresh Sanghani*, Sonal Sanghani* * Department of Biochemistry and Molecular Biology Mahesh Merchant Indiana University School of Informatics mmerchan@iupui.edu
Graduate Programs 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
Data Integration Laboratory Information Management Systems (LIMS) Electronic Laboratory Notebooks (ELNs) Data Visualization In-house Databases Enterprise Resource Planning, SAP
The integration challenge Lab instrumentation Data sources Office applications Print and file data LIMS Visualization and analytics software E-Notebooks Discovery Databases Data consumers 2004 Waters Corporation
Software at Indiana University 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)
ELN in a Classroom 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 - Gene Expression Project
ELN Metadata Definition
ELN Data Visualization
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 Data Visualization
ELN Daily Log of Problems Encountered
ELN Database Queries
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 Lab instrumentation Data sources Office applications View Waters NuGenesis SDMS Extract Lims Visualization and analytics software E-notebooks Discovery and clinical Databases Data consumers 2004 Waters Corporation
elab Notebook View of SDMS Data HPLC NMR 2004 Waters Corporation
SDMS Data from elab Notebook SDMS Vision Data Source Select Data to View Data is selected then sent to the elab Notebook 2004 Waters Corporation
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