IT Infrastructure & Informatics: Collaborative Software, Standards & Web Technologies

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Data sharing, linking data sets, accessing data, and archiving in collaborative environments are creating new challenges for informatics and software experts across the drug discovery and life science industry. Data protection, privacy and security issues need to be considered carefully as more pharmaceutical companies and academic centers find themselves sharing data and information both within their own organization and with outside collaborators. This track will highlight some of the strategies and software tools being employed across the life sciences to deal with the growing need for data sharing. Implementing standards to reach process efficiency and interoperability will also be addressed, along with ontologies and web technologies.

WEDNESDAY, 6 OCTOBER

13:00 Conference Registration

 

Data Integration And Collaboration

14:00 Chairperson’s Remarks

14:05 Knowledge Engineering: Integrating the External
with the Internal

Ian Dix, Ph.D., Capability Lead for Knowledge Engineering & Information Science, Discovery Information, AstraZeneca

Decision-making within R&D is often compromised by the sheer volume and heterogeneity of decision-relevant biomedical & commercial information available to project teams: project teams struggle to access critical information in the necessary time, at an acceptable quality, coverage, and cost. This challenge is compounded by the formats and accessibility of biomedical information, with the most valuable information being ‘locked’ within textual formats such as the literature, patents and internal reports. This BioIT presentation will describe AZ’s response to this challenge, focusing on external content delivery.  The presentation will be divided into 4 parts: 1) a synopsis of the information challenge; 2) an overview of AZ’s existing capability; 3) an insight into AZ’s emerging capabilities to transform external & internal information integration and delivery; 4) the need for pre-competitive standards and approaches to develop the next generation external information services.

14:35 The Reality of Web Services in the Life Sciences

Carol GobleCarole Goble, Professor of Computer Science, University of Manchester

Finding and using web services to third party online bioinformatics resources is much harder than it should be. This talk will describe the current reality of Web Services in the Life Sciences, and how better practices can be encouraged. BioCatalogue provides a common interface for registering, finding, and monitoring bio-web services and will be described here.

15:05 The New Information Landscape: Towards a New Logic and Practice to Enhance Interoperability and Collaboration in Life Science

Mats Sundgren, Ph.D., Principal Scientist, Global Clinical Development, AstraZeneca R&D

Today the pharmaceutical industry needs to transform itself on many levels to enhance scientific research and innovation output. In order for the pharmaceutical industry to succeed in new research areas like personalized medicine and predictive medicine, one key factor is how to connect their internal information with the external world, including health care and patients, to share and make use of different information types or systems. Today, the pharmaceutical industry world of information can be divided into three domains. First the “internal information domain”, here we build and refine scientific information that shapes our future products. Secondly, the “external regulated information domain”; here with limited access we connect to scientific databases and health information (e.g. clinical trials). And last, the “external open information domain”; this fast moving external open domain, accessible through the Internet, is becoming a vital source of providing strategic value regarding safety and science information (e.g. scientific discussion forums, patient communities, blogs). From a new drug development perspective, the competitive edge is therefore the ability to connect all three information domains.

15:35 Refreshment Break

 

CASE STUDIES OF OPEN COLLABORATIONS AND OPEN SOURCE SOFTWARE

Sponsored by
Accelrys
16:00 A Scientific Platform for Enhancing Research and Development Productivity and Innovation

Rob Brown Robert Brown, Ph.D., Senior Director Life Sciences, Accelrys Inc.

This talk will discuss the use of the Accelrys informatics platform to enhance research and development productivity and innovation. Managing end-to-end scientific workflows in a unified informatics platform allows research and development organizations to:
Streamline their operations and reduce operating costs
Increase the potential for innovation through timely capture of information, enhanced collaboration and informed decision making

16:30 Collaborative Development of a Registration System for Biologics

Jeremy Packer, Ph.D., Head, Bioinformatics, Abbott

In collaboration with Accelrys and other pharma companies, we have developed a registration system that meets the special requirements of biologics. Proteins (including antibodies), plasmids and cell lines are assigned corporate identifiers according to business rules that define uniqueness appropriately for their class. Features of the software and factors that led to the success of the collaborative venture will be described.

17:00 Building Tools for Collaborative and Open Projects in Biology

Lars Jorgensen, Senior Scientific Manager, Production Software, Sequencing Informatics, The Wellcome Trust Sanger Institute

Building tools to support research consortiums and flat research organizations poses a number of challenges. Requirements are often very open ended and the tools are used by a large number of different types of users, from Ph.D. students to dedicated informatics staff. This talk will describe the tools and processes we use to tackle these challenges. 

18:30 – 21:00 BIOTECHNICA Night: Beer Hall, Full Dinner Reception, Live Band

(Please register to reserve your complimentary ticket ahead of time. No tickets will be available on-site.)

THURSDAY, 7 OCTOBER 

9:00 Conference Registration and Morning Coffee

 

IMPLEMENTING STANDARDS TO REACH PROCESS EFFICIENCY AND INTEROPERABILITY – METADATA AND BEYOND

9:30 Chairperson’s Opening Remarks

9:35 MIBBI: Minimum Reporting Guidelines for Bioscientists

Chris Taylor, Ph.D., Senior Technical Officer, The European Bioinformatics Institute

The last ten years have seen significant progress in various bioscience fields towards standardized guidance for reporting public research, aiming to raise the annotation quality and utility of publicly-available bioscience data. MIBBI integrates the outputs of that (necessarily piecemeal) development, presenting users with a unified set of guideline ‘modules’ that can easily be assembled and accessed in various forms.

10:05 Is the Cloud the Panacea for Process Efficiency?  The Elastic-R Case Study

Karim Chine, Director, Cloud Era Ltd.

Elastic-R provides a platform for real time collaboration and for resource sharing in the cloud. By defining simple contracts and by providing user friendly tools for the production, sharing and reuse of all the artifacts of computing (libraries, user interfaces, spreadsheets, servers, data analysis sessions,  etc.), it intends to create a new eco-system for computational sciences that would be highly beneficial to the life sciences protagonists. Generic computational engines, based on R, Scilab, Python, etc.  can be hosted by virtual machines running on Amazon Elastic Cloud, on private clouds or on HPC infrastructures. The engines are stateful, interoperable and remotely accessible from standard Restful Web Services. They allow user friendly high-throughput computing and collaborative data analysis. Researchers can use them to create and distribute dashboards on top of models and data. Automatically generated macro- enabled Word documents and Excel workbooks can be synchronized in real-time with those engines: in a familiar office environment, scientists can view and update common data sources and can seamlessly call data processing services in the cloud.

10:35 Coffee Break


11:00 Now-Generation Data Transport Technology for Life Sciences: Keeping Pace with InnovationSponsored by
Aspera

Xingzhe Fan, Ph.D., Research Scientist, Aspera, Inc.
Collaborative research teams need to efficiently exchange, process and analyze gigabytes of data in a sequence run. Traditional data transport methods are unable to manage this volume of data. This session focuses on now-generation transport technologies used in genomic research that achieves up to 1000x the throughput of standard file transfer protocols. A case study of global researchers participating in the 1000 Genomes Project showcases how they have been able to exchange sequencing data at 1 Gbps.

11:30 iSee - Dissemination of Structural Biology Data to the Masses
Brian Marsden, Ph.D., P.I., Research Informatics, Structural Genomics Consortium, University of Oxford
Making structural biology data accessible to non-structural biologists is key to ensure that structural information is considered during a chemical probe development or drug discovery project. In collaboration with MolSoft LLC, the SGC has developed an intuitive and interactive platform called iSee that integrates structural biology methods into a 3D document. This platform and our data is freely available online.

 

ONTOLOGIES AND STATE-OF-THE-ART WEB TECHNOLOGIES

12:00 Semantic Data Integration for Translational Research in Neuroscience

Rudi Verbeeck, Ph.D., Program Manager, Informatics Center of Excellence, Janssen Pharmaceutical Companies of Johnson & Johnson

To support translational research, we are evaluating the potential of semantic web technology to integrate data from discovery research through to the clinical environment in the area of neuroscience. We present our architecture for data source description and discovery and for query generation. A key component of the architecture is a central ontology that defines common entities used in data source mapping.

12:30 Lunch for Purchase in the Exhibit Hall

13:45 Dedicated Poster Viewing in the Exhibit Hall

 

 

Ontologies And State-Of-The-Art Web Technologies Cont’d

14:30 Chairperson’s Remarks

14:35 Keeping Track of Data and What the Data Are About: An Exploration in Realism-Based Ontology for Translational Research

Werner Ceusters, Ph.D., Director, Ontology Research Group, NYS Center of Excellence in Bioinformatics & Life Sciences

The Innovative Medicines Initiative (IMI) is a unique pan-European public and private sector collaboration between large and small biopharmaceutical and healthcare companies, regulators, academia and patients. The aim of IMI is to support the faster discovery and development of better medicines for patients and enhance Europe’s competitiveness by ensuring that its biopharmaceutical sector remains a dynamic high-technology sector. One specific aim is to create a Knowledge Management Platform to arrive at effective data integration and analysis tools. Ontology has been recognized to be an important corner stone. In our presentation, we will discuss the exact place of ontology in such an endeavor and its relationship to terminologies and information models.

Sponsored by
Infosys sm 
15:05 Shared Molecular Network Models of Unrelated Diseasomes – Unraveling the Conundrum of Network Medicine

Dr. Reena Gollapudy, Lead Consultant, IHL, Infosys Technologies Ltd.
An understanding of the functionally relevant genetic, regulatory, metabolic and protein-protein interactions in a cellular network play an important role in deciphering the pathophysiology of human diseases. Several diseases share common pathophysiological mechanisms. Identification of common pathophysiological pathways between seemingly unrelated diseases could offer new approaches to drug discovery. The use of network and systems biology in generation of common diseasomes and identification of shared molecular pathways holds great promise in advancement of drug discovery approaches with specific relevance to molecular repurposing, predictive toxicology and discovery of diagnostic biomarker properties of pharmaceutical drugs and candidate molecules. This treatise attempts to explore common diseasome attributes and applications using a proliferasome as a case study.

15:35 Refreshment Break

16:00 Sponsored Presentation (Opportunity Available)

16:30 How Can a “Normal End User” Become a Web Service Consumer?

Christian Hauck, Ph.D., Knowledge Management and Competitive Intelligence, Novartis Pharma AG

Web services exist in various variants, but are mostly used by experts to build machine-to-machine interfaces. Without enough consumers, providers don’t add value. Without enough providers, consumers get no value. We try to build web service consumer “frontends” for educated scientists and business people to help overcome this “chicken-and-egg” bootstrap problem. Attendees will learn about how to re-use web services that might already exist in their organizations, thereby creating more value out of what is already available.

17:00 Efficient Web-Browsing for the Life Scientist

Reinhard Schneider, Ph.D., Team Leader, Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL)

Anyone who regularly reads life science literature often comes across names of genes, proteins, or small molecules that they would like to know more about. We have developed a new service called Reflect (http://reflect.ws) that can be installed as a plug-in into browsers. Reflect tags gene, protein, and small molecule names in any web page, typically within a few seconds. Clicking on a tagged gene or protein name opens a popup showing a concise summary that includes synonyms, database identifiers, sequence, domains, 3D structure, interaction partners, subcellular location, and related literature. The popups also allow navigation to commonly used databases. The project won the first price in the Elsevier Grand Challenge competition and is used to annotate online issues of the Journal "Cell". As another application of the infrastructure we will show a half-automatic system, which is able to map mutational information from text sources to database sequences and 3D structures.

17:30 A Data Warehousing Approach for the Management of Clinical and Operational Information: Specific Challenges within Pharma Development

Norbert Fritz, Ph.D., Development Lead, Business Intelligence Warehouse, Information Management - Product Development Operations, F. Hoffmann-La Roche Ltd

The development of new medicines implies more and more extensive generation and usage of medical information. Management of this broad scope of information requires integration of data generated in heterogeneous data sources and presentation of clinical and operational data in one consolidated data model. Specific challenges for Pharma Development include amongst others: evolving and changing medical concepts, disparate systems generating source data, disparate data models and standards within various data sources, transient data quality issues, the need for frequent data refreshes. The presentation will analyze the specific challenges, present approaches to design adequate solutions and discuss real-life experiences from a Data Warehousing project.

18:00 Close of Conference



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