enabling connectivity in electronic laboratory notekeeping

12.06.2018 ELN Workshop Berlin Leibniz 1

Enabling connectivity in electronic laboratory notekeeping

A pilot approach in biomedical sciences

SFB 1002/1190 INF team


Challenges: Introduction of an ELN in academic researchenvironments

• No routine workflows (basic research)

• Dynamic working structures (heterogeneous methodology)

• High dynamics of interdisciplinary team composition

• Data management/access policies rarely defined


Research Data PlatformIntegrative Data Management

CRC 1002Research Data Platform

• Collection and interconnection

of research data used in

publications

• Persistent resolvable access

and long-term re-usability of

CRC 1002 data

• Data standardization for

submission to public

repositories

• Data access: Development of

Use & Access Policies


ELN organization Cross-linking data in an ELN

Mouse Line

Catalogue

Antibody

Catalogue

Cell Line

Catalogue

Echo

Data

RSpaceRSpace

Published Data

Registry

Research Group

Filestores

Web Resources

(Databases, Catalogues)

Research Group

Databases


ELN organization Example: Cross-linking data in an ELN


ELN organization Research group representation

1. Community (optional)

2. PI

3. Lab Manager

4. User (Scientist)

Research Group 1

1. Community (optional)

2. PI

3. Lab Manager

4. User (Scientist)

Research Group 2

CRC 1002

(Scientific Consortium)

Cooperation

sharing sharing


ELN organization Structuring data in an ELN

a. Chronologically

DiaryDiary

Day 1Day 1

Exp 1aExp 1a

Exp 2Exp 2

Day 2Day 2

Exp 1bExp 1b

Exp 3Exp 3

Method 4Method 4

b. Project-oriented c. Method-oriented

Lab …Lab …

Project 1Project 1

User 1User 1

Exp 1Exp 1

Exp 2Exp 2

User 4User 4

Exp 1Exp 1

Exp 2Exp 2

Project 2Project 2

User 1User 1

Exp 1Exp 1

Exp 2Exp 2

Exp 3Exp 3

User 2User 2

Exp 1Exp 1

Lab…Lab…

Methods(SOPs)

Methods(SOPs)

PCRPCR

Agarose-Gel

Agarose-Gel

CytoCyto

ResultsResults

PCRPCR

Agarose-Gel

Agarose-Gel

CytoCyto


ELN organization Restricted access


ELN organizationWorkspace


ELN documentationUnstructured documentation

• New methods

• Room for “creativity”


ELN documentationStructured documentation

• Centralized protocols

• Learning tool

• Quickly shared

• Metadata recording facilitated


ELN documentationInstitutional filestore connectivity

• Cross-linking of primary research data

• Enables remote access to lab data

• Exports contain automatic lists of cross-linked data


ELN documentationSustainability

Audit Trail



ORCID integration



Easy additional reusable archiving strategies:

Regular Data-Exports

Most similar to paper, partially interactive => PDF-Format

Most similar to ELN (Rspace), interactive => HMTL-Format

Interoperability, human and machine readability => XML-Format

Interfaces to repository software (e.g. Dataverse, DSPACE)



Dataverse Connection


Dr. Sara Nußbeck

(TP INF-Leader IT)

Prof. Dr. Blanche Schwappach

(TP INF-Leader Research)

Dr. Harald Kusch

(PostDoc)

Markus Suhr

(B.Sc. Inf)

Dr. Evelina De Laurentiis

(PostDoc)

CRC 1002/1190 INF team

orcid.org/0000-0003-1223-6494 orcid.org/0000-0003-0225-6432

orcid.org/0000-0002-6469-1627 orcid.org/0000-0002-9895-2469 orcid.org/0000-0002-6307-3253

Georg Aschenbrandt

Luca Freckmann

Christian Henke

Sophia Rheinländer

Björn Hansen


ELN implementationChallenges

• Start up phase

Takes some time

• Familiarize

Ideal vs reality


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enabling connectivity in electronic laboratory notekeeping

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