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Investigating Provenance in Cell Biology 
Tutorial 
 
June 2014, Cologne,  Germany 


Objectives:

This tutorial will investigate the following themes:

Introduce the idiosyncratic nature of cell biology research and the importance of reproducibility, cell and tissue analytics, 
cell therapy development and method/protocol documentation.

Outline current informatics approaches in cell biology, e.g. ISA, MI formats etc.

Identify why textual information and visual representation of provenance is important in this application area. 

Identify the relationship between practice and provenance.  

Identify differences between methodology workflow and methodology design and embedded navigation capability (spatiotemporal complexity)

Outline mechanism/algorithms to assess best practice and associated outcomes in quantifiable terms.

Identify Challenges for the use of provenance in manufacturing environments compared to discovery environments.

Describe the current culture of documentation – in terms of diversity, language and mechanism scribbles to word docs used in cell biology research.

Provide a case study of stem cell research – making use of multi-faceted  tools and approaches for incorporation of systematic documentation/tacit knowledge and trust 

Duration & Format:

This 3 hour tutorial is expected to be an interactive session, with significant discussion between the presenters and the audience.

There will be an initial 1.5 hour presentation (by Khan, Errington and Rana), followed by a 45 minute break out session (into three groups). This is then followed by a "bringing it together" session of 45 minutes. 

A key outcome is expected to be the identification of key challenges for provenance recording, annotation, storage and analysis in cell biology. 


Intended audience:

This event is primarily targeted towards computer scientists to identify the state of irreproducibility in biological sciences, especially in cell biology.  The organisers will provide a number of key challenges that could stimulate work in the use of the recent PROV model from W3C and potential tools that could be benefit to cell biologists.  Two key aspects:

  1. Understanding the documentation and utilisation of experimental information culture within the biological community – in particular with reference to cell biology, based on the experience of the presenters.
  2. How provenance can play a critical role (understanding, assessment of sample/data quality, reproducibility) in cell biology research. 


About the presenters:

Dr Imtiaz Khan is a Marie Curie International Outgoing Fellow, working collaboratively with Broad Institute of Harvard and MIT, USA and Cardiff University, UK. He is the lead developer of virtual laboratory work environment – ProtocolNavigator (PN) that enables the design, capture, exploration and sharing of experimental protocols through a visual map with contextual links to the resulting data. 

Rachel Errington is currently a Professor in BioMolecular Imaging and Systems Cytometry at Cardiff University, leading a multi-disciplinary R&D programme focused on biophotonics and predictive cancer biology. Rachel is an entrepreneur and director at Biostatus Ltd, a UK biotechnology developing novel fluorescent probes and tools for cell-based assays.

Omer Rana is Professor of Performance Engineering at Cardiff School of Computer Science & Informatics. He was formerly the deputy director of the Welsh eScience Centre at Cardiff University -- where he had an opportunity to collaborate with a number of scientists working in computational science and engineering. He was involved in two projects investigating provenance in service-oriented architectures: the UK EPSRC-funded PASOA (Provenance Aware Service-Oriented Architecture) and the European “Grid Provenance” project. 


ProtocolNavigator
Part of the ProtocolNavigator project