1. Environmental Molecular Sciences Laboratory Electronic Laboratory Notebook Elena S. Mendoza 5/19/98 Environmental Molecular Sciences Laboratory Computing & Information Sciences Pacific Northwest National Laboratory

2. Environmental Molecular Sciences Laboratory Overview Project Background What is an “Electronic Notebook”? How does it work? API’s Technologies Wrap-up

3. Environmental Molecular Sciences Laboratory Projects Collaboration Management (ANL, PNNL): Real-Time Session Management from both a session based metaphor and a space based metaphor. Electronic Notebooks (LBNL, ORNL, PNNL): We’re developing an Electronic Notebook system to provide a shareable, multimedia version of the traditional paper scientific notebook. Collaboratory Interoperability Framework (ANL, LBNL, PNNL, SNL): Technologies to allow scientific instruments, notebooks, and real-time collaboration tools to work together. Structural Biology LDRD Researchers collaborating electronically to perform NMR experiments. DOE2000 EMSL Operations Use of the Collaboratory tool suite as a portion of the EMSL Research Facility.

4. Environmental Molecular Sciences Laboratory Collaborative Electronic Notebook Systems Association (CENSA) Rich Lysakowski - www.censa.org Chemical and Pharmaceutical companies promoting the development of commercial EN systems

5. Environmental Molecular Sciences Laboratory DOE2000 Electronic Notebook Project LBNL ORNL PNNL

6. Environmental Molecular Sciences Laboratory DOE2000 EN Approach Started with 3 separate prototypes at 3 labs Defined common architecture and all are migrating towards it (e.g. editor interface, import/export) Providing prototypes and support now(install, docs, help, SDKs,...) New functionality available every ~6 months Revolutionize over 3 years

7. Environmental Molecular Sciences Laboratory Types of Notebooks/ Purposes of a Notebook Researcher’s Laboratory Notebook (Scientific Observations) Design Notebook (New Ideas) Instrument Log Book (Maintenance) Experiment Log Book (Time/Cost Accounting) Legal Record –Invention Reports (Intellectual Property) –Sample Tracking Notepad Group Workspace

8. Environmental Molecular Sciences Laboratory Sources of Notebook Information Instruments, Analysis/Visualization/Modeling Software –Data files/ Results files in ‘native’ format (lossless) –Summaries - Images, Tables, …(lossy) –Metadata/ Processing history/ Parameter files Researchers (individual) –Notes - structured and unstructured text –Sketches/ Diagrams/ Schematics Groups –Presentations –Conversations(A/V, Whiteboard, Shared Screeen, …)

9. Environmental Molecular Sciences Laboratory EMSL Electronic Notebook WWW based access to EMSL data and meta-data Automation of data/metadata input from instruments and calculations Querying/ Searching Simple, secure access to full datasets Interactive input of results into notebook from the WWW Rich media types (text, images, files, 3D structures, voice, animations, video,...) Extensible - 3rd party API for new data types

10. Environmental Molecular Sciences Laboratory A Common Architecture Notebook Client Common Input Editors/Viewers Text Images Equations Sketches Data Type N... OODBMS RDBMS Files Common Notebook Engine Data Storage Interface Resource Discovery Signing... CORBA HTTP JAVA Advanced Features Data Acquisition Systems (many) Input interfaces (few) migrated Advanced Features

11. Environmental Molecular Sciences Laboratory How Does it Work? Server - Perl/cgi –generates html on the fly Client - java –application and/or applets Communication –Sockets and http Security –DFSWeb/cookies –Signed Applets/Certificat es –SSL - https Export/Import –multi-part mime

12. Environmental Molecular Sciences Laboratory Object Diagram INOb NOb NObList 1+

13. Environmental Molecular Sciences Laboratory NOb Interface package eln.nob; import java.lang.*; import java.io.*; import java.awt.*; import java.util.*; public interface INOb { public Object get(String key); public Object put(String key, Object value); public Enumeration keys(); public void remove(String key); }

14. Environmental Molecular Sciences Laboratory Notebook Object Fields String authorName String objectID String dateTime String label MIME dataType Byte data[] URL dataRef Version OID Instrument ID Author Certificate Author DN NB Engine DN NB Certificate Signature - author Signature - witness Signature - timestamp Defined TBD (non-standard)

15. Environmental Molecular Sciences Laboratory Notebook Objects and Editors

16. Environmental Molecular Sciences Laboratory Editor/Viewer API Bean like Extensible - add editors to the CLASSPATH Add editors on the fly Render any “type” of data public interface INBEditor { public Image getIcon(); public String getLabel(); public void Launch(INOb aNOb); public void setClient(INBClient aClient); }

17. Environmental Molecular Sciences Laboratory Viewer Interface

18. Environmental Molecular Sciences Laboratory Signed Applets Sandbox - How to get out of it Capabilities API try { PrivilegeManager.enablePrivilege("UniversalPropertyRead"); PrivilegeManager.enablePrivilege("UniversalFileRead"); } catch (netscape.security.ForbiddenTargetException e) { System.err.println("\tFailed! Permission to read system properties denied by user."); } catch (Exception e) { System.err.println("\tFailed! Unknown exception while enabling privilege."); e.printStackTrace(System.err); } > signtool -k emslCertificate -Z ClientApplet.jar.

19. Environmental Molecular Sciences Laboratory Certificate Example

20. Environmental Molecular Sciences Laboratory LiveConnect Talking from Java to JavaScript –JSObject jsroot = JSObject.getWindow(theApplet); – JSObject jsdocument = (JSObject)jsroot.getMember("document"); Using JavaScript to get and set cookies public String getCookies() { Object tmpCookies = mJsDocument.getMember("cookie"); String cookies = tmpCookies.toString(); return cookies; } public void setCookies(String[] theCookies) { mJsDocument.setMember("cookie", theCookies[0]); mJsDocument.setMember("cookie", theCookies[1]); }

21. Environmental Molecular Sciences Laboratory Export/Import Export Nobs and NobLists to well-defined multi-part mime Read and write Mime from Java Use internally written encoders/decoders

22. Environmental Molecular Sciences Laboratory Current Team Members EMSL Collaboratory Details Jim Myers Brett Didier Ken Yates Elena Mendoza Shelly Harris Shawn Merriman Debbie Payne Tom Valdez Kelly Keating Ray Bair http://www.emsl.pnl.gov:2080/docs/collab Web Address

23. Environmental Molecular Sciences Laboratory For more information Java-dev@emsl.pnl.gov C&IS Technical Exchange 5/19/98 9:00am EMSL Send me mail http://www.emsl.pnl.gov:2080/docs/collab

24. Environmental Molecular Sciences Laboratory Acknowledgments U.S. Department of Energy –Mathematical, Information and Computational Sciences Division of the Office of Energy Research –Office of Biological & Environmental Research of the Office of Energy Research –Pacific Northwest National Laboratory (PNNL) Laboratory Directed Research and Development (LDRD) Pacific Northwest National Laboratory is a multiprogram national laboratory operated by Battelle Memorial Institute for the U.S. Department of Energy under Contract DE-AC06- 76RLO 1830.