Trip Report: E-WorkBook, BioBook, ChemBook, July 2009

work in progress --Andreas Gros 09:39, 3 August 2009 (UTC)

These notes were taken by Andreas Gros during a two day workshop at IDBS, Guildford, UK.

Date[edit]

30/31 July 2009

Place[edit]

IDBS, Guildford, UK

Topics[edit]

Introduction to the E-WorkBook Suite: http://idbs.com/ELN/

E-WorkBook: http://idbs.com/eln/e-workbook/
BioBook: http://idbs.com/eln/biobook/
ChemBook: http://idbs.com/eln/chembook/

E-WorkBook[edit]

E-WorkBook is a flexible and configurable science-neutral electronic lab notebook geared towards all basic research. Capture any data type from disparate sources under one secure portal including instrument data, LIMS content, statistical analysis, graphical data, text-based objects and human observation. E-WorkBook automates data capture and storage and provides simple and fast report creation, allowing greater productivity for the research scientist.

Aspects

easy data/image import and export via varios pathways including web services and drag&drop and mulitple formats (XML, MS Office, PDF, and many others)
flexible and rigid workflows for experiments via templates with options for configurable input forms
special workflows to have experiments reviewed by a supervisor/colleague or for requesting comments; these tasks go into the E-WorkBook inbox of the respective supervisor/colleague, but can also be sent by e-mail.
all results are searchable in a very comprehensive way
easy instrument output integration/import via "watched folders" and increasing RS232 integration
data can be directly fed into text module templates so that for example facts in publication abstracts and conclusions can be updated accordingly, which speeds up reporting and result publication
complete versioning of everything (with complete roll-back possibilities)
experiment sign-off
complete audit trail of all activities
supports controlled vocabularies / ontologies (in IDBS terms, the catalogue)
interface extendable with Eclipse plugins, e.g. for custom value pickers, fetching data from external controlled vocabularies (CVs), renderers for more data types and file formats and web service incorporation
columns in results tables are mapped to terms in the catalogue (an ontology); in case something is a measure, values go into a facts table with the context (treatment groups, etc.) of the experiment linked to it in various other tables in a star-like structure.
all files are being stored in an Oracle DB, large files can be handled by an attached file server -- in this case just the metadata is stored in the Oracle DB + a link to the file on the server
integrates well with LDAP/ActiveDirectory for user authentification

BioBook[edit]

BioBook is an extension to E-WorkBook which brings complete electronic study and data management. BioBook aims at enhancing the productivity of biologists by managing every stage of the study lifecycle. From experimental set up and data capture, through statistical analysis, curve fitting, and advanced graphing, to report creation, sign-off and publication. BioBook simplifies the management of complex research data.

it can make use of various statistics packages (among others, also R)
spreadsheet has both statistical and graph fitting capabilities built in
it provides flexible, quick, and semi-automated data visualization possibilities

ChemBook[edit]

ChemBook is a chemically aware environment, which allows chemists to draw reaction schemes and structures, calculate stoichiometry, enumerate parallel synthesis reactions and register compounds into corporate registration systems. The solution also allows researchers to execute standard chemistry searches (SSS, exact, similiarity) for products and reactants, and reaction transformations, in a complete research management environment for chemists.

Roadmap for further developments[edit]

The next version of the E-WorkBook suite will have (among others)

enforced workflows (enforced in the sense of a step-wise fulfilment checking procedure)
explicit Prism support
batch printing of experiments
extended RS232 integration for machine support
data import of large datasets
mandatory cells in spreadsheets
label printing for flasks, etc.
integration with MS Outlook

User input is taken into consideration for further development of the software.