Electronic Laboratory Notebook in the Graduate Level Laboratory Informatics Program
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1 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
2 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
3 Data Integration Laboratory Information Management Systems (LIMS) Electronic Laboratory Notebooks (ELNs) Data Visualization In-house Databases Enterprise Resource Planning, SAP
4 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
5 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)
6 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
7 ELN - Gene Expression Project
8 ELN Metadata Definition
9 ELN Data Visualization
10 ELN Data Visualization
11 ELN Conclusions
12 ECMS Project Layout
13 ECMS Metadata
14 ELN Protein Data Bank Project
15 ELN Questions to be addressed
16 ELN Project Outline
17 ELN PDB File Parser
18 ELN Database
19 ELN Data Visualization
20 ELN Data Visualization
21 ELN Daily Log of Problems Encountered
22 ELN Database Queries
23 ELN Database Queries
24 ELN Results and Discussion
25 ELN Conclusions
26 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
27 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
28 ELN Laboratory Handouts and Analysis
29 ELN Adding Comments with a Tablet PC using Ink Window
30 ELN Laboratory Comments
31 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
32 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
33 elab Notebook View of SDMS Data HPLC NMR 2004 Waters Corporation
34 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
35 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
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