Environmental Molecular Sciences Laboratory Electronic Laboratory Notebook Elena S. Mendoza 5/19/98...

Environmental Molecular Sciences Laboratory

Electronic Laboratory Notebook

Elena S. Mendoza

5/19/98

Environmental Molecular Sciences LaboratoryComputing & Information Sciences

Pacific Northwest National Laboratory


Overview

• Project Background

• What is an “Electronic Notebook”?

• How does it work?

• API’s

• Technologies

• Wrap-up


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.


Collaborative Electronic Notebook Systems Association (CENSA)Rich Lysakowski - www.censa.org

Chemical and Pharmaceutical companies promoting the development of commercial EN systems


DOE2000 Electronic Notebook Project

LBNL

ORNL

PNNL


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


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


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, …)


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


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 DiscoverySigning...

CORBAHTTPJAVA

Advanced Features

DataAcquisitionSystems (many) Input interfaces (few)

migratedAdvanced Features


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/Certificates

– SSL - https

• Export/Import

– multi-part mime


Object Diagram

INObINOb

NOb

NObList1+


NOb Interfacepackage 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);

}


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)


Notebook Objects and Editors


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);

}


Viewer Interface###PAR### file viewer######### ProcPar: Viewer for Varian NMR procpar files######### Jim Myers 3/98sub rend_par{ local($filename) = @_; local($visvar); #Clear the visualization variable. This holds rendered content. $visvar = “”;

#Parse out just the name of the file itself from the $filename variable (which includes path info) if ($filename =~ m#.*/([^/]*)$# )

{local($filen) = $1;

$visvar .= “<hr>”;$visvar .= “<center><table border=1 width = 400 height = 150><td>\n”;$visvar .= “<applet codebase=\”$server$relapplets/procpar\” code=nmr.Pro

cpar”;$visvar .= “\r\nARCHIVE = \”procpar.jar\”\r\n”;

$visvar .= “ width = 400 height = 150 vspace=0 hspace=0>\n”;

$visvar .= “<param name=ProcParURL value=\”$server$relnotebook/$notebook/$folder/$experiment/$filen\” >\n”;

$visvar .= “<param name=NumLines value=\”5\” >\n”;

$visvar .= “The Procpar viewer applet is not responding, is java enabled ?\n”;

$visvar .= “</applet>\n”;

$visvar .= “</table></center>\n”;

} else {##cgierror(“OUCH: can’t find filename in: $filename” );

$visvar .= “<P>Sorry, can’t find usable filename in: $filename<P>\n”;

}$visvar;

}1;

_.


Signed Applets• Sandbox - How to get out of it

• Capabilities APItry { 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 .


Certificate Example


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]); }


Export/Import

• Export Nobs and NobLists to well-defined multi-part mime

• Read and write Mime from Java

• Use internally written encoders/decoders


Current Team Members

EMSL Collaboratory Details

Jim MyersBrett DidierKen Yates

Elena MendozaShelly Harris

Shawn Merriman

Debbie PayneTom Valdez

Kelly KeatingRay Bair

http://www.emsl.pnl.gov:2080/docs/collabWeb Address


For more information

• [email protected]

• C&IS Technical Exchange 5/19/98 9:00am EMSL

• Send me mail

• http://www.emsl.pnl.gov:2080/docs/collab


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.

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