Transcript Bioinformatics Service Core

Bioinformatics Service Core
OVERVIEW
The Indiana University School of Medicine (IUSM) Bioinformatics Service Core
started in 2007 in the Center for Computational Biology and Bioinformatics. Sean
Mooney (Department of Medical and Molecular Genetics) leads the informatics
infrastructure and projects for the Core while Lang Li (Division of Biostatistics) leads
the analytical services.
We are an IUSM and an Indiana Clinical and Translational Sciences Institute
(IndianaCTSI) approved service core. We have been operating for 2 years serving
basic and clinical researchers through web application development, data analysis,
graphic design, and more. Through our diverse resources and personnel, a mature
development environment, and our dynamic project scope we are able to serve a
diverse set of researchers with rapid development and quality solutions to many
biological, clinical, and informatics problems.
RESOURCES
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Service cores in various disciplines are being initiated in medical schools and
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universities across the country with the intention of serving principal investigators
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through many services including microarray experiment execution, data analysis,
visualization, and software development. We present the development of the
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Bioinformatics Core at Indiana University School of Medicine, lessons learned, and
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best practices implemented.
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We present example projects with a simple explanation of core operations, and
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lessons learned in establishing new projects, collaboration, project development, and
advertising. We also discuss practices we've adopted in development, analysis, and
technology.
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The challenge
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One of the primary challenges facing informatics service units on medical school
campuses is providing service to small day-to-day activities as well as meeting the
significant challenge of cyber-infrastructure that is large national informatics
networks. Campuses need to invest heavily in adopting to large informatics networks
(such as caBIG, BIRN, etc), however, there is often few, if any resources to actually
invest in this infrastructure.
Projects
Examples of projects we have undertaken include development of web-based tools,
databases, analytical pipelines and analytical consulting services.
RESEARCH CONTRIBUTION HIGHLIGHT
LIST OF SERVICES
Example Sites
Bioethics Library - IU School of
Medicine
http://bioethics.iupui.edu/
Academic Association of Biologics
Manufacturers
http://aabmonline.org/
Indiana Clinical and Translational
Sciences Institute
http://indianactsi.org/
• Biomedical Data Management
• Graphic/Web Design
• Consulting
Preferred Platforms
Platform
Linux/Apache/MySQL/PHP – Although
we also support sites in Python, Perl,
Java and ColdFusion
• Community & Training
Framework
CakePHP – MVC programming in PHP.
Also use Drupal and Joomla.
• Tool Access
Workflows
Python and/or Perl
Our projects include web-based data analysis tools, commercial web sites, cross-institutional sites, and collaborative
workspaces. We easily adapt to provide novel features for clients and are able to develop efficiently even on new
frameworks (i.e. Joomla) and provide professional quality graphic design.
Supported Analysis
Proteomics
Microarray
SNP Arrays
Pharmacogenetics/Correlative-Studies
Sequence analysis/next generation sequencing
Metabolomics
Molecular/physiological static/dynamics network models
Text mining
Database access
Custom built tools
As with all projects in the Core, each project is executed by a staff member with updates and results reviewed by a
faculty researcher. Analysis generally results in a report containing a verbal, laymen explanation of the data, the analysis
algorithms, and further publication-ready text as the client requests. The report also contains images portraying the data
set, visually answering questions posed by the client or staff member, and publication quality images where applicable.
Lastly the report is returned with any intermediate or interesting data set (i.e. specific gene lists applicable to a given
microarray experiment, pathway details, et cetera).
Analytical consulting for many high-through data platforms have been matured enough for routine analysis services, such
as micoarray, proteomics, SNP array, pharmacogenetics, sequence-analysis / next-generation sequencing, molecular /
physiological static / dynamics network models, text mining. Most of the work flows have been built within
BioConductor. Metabolomics is the only area that needs further development.
Funding
The Core was established with startup funds provided by the Center for
Computational Biology and Bioinformatics. Our continued operation is funded by
ongoing hourly and percent effort projects.
Future
We hope to continue to aid basic and clinical researchers through existing and novel
services in the future. We recognize several areas, including large scale data
integration/ annotation, online collaboration spaces, and rapid genotyping, as areas of
future service. We seek future clients and projects by presenting our mission and
passed work at faculty meetings, seminars, conferences, and events throughout our
campus.
• Data Analysis
In order to facilitate analysis of these high-throughput data sets the Core has licensed several pieces of software. Pathway
Studio (http://www.ariadnegenomics.com/) and Ingenuity Pathway Analysis (IPA, http://www.ingenuity.com) are used for
understanding data in a systems biology context. The IPA license purchased allows the Core to use the tool for analysis
and also sub-license it within the School of Medicine – making IPA far more affordable for research labs. For those labs
purchasing an IPA license, the core offers training and a first line of support.
QUALITY CONTROL AND ASSURANCES
We are completely soft funded. That means all of our service projects are billable. For
short projects (less than 150-200 hours), we bill hourly at $50/hr. For longer term projects,
we bill as a percent of effort of a Core staff member. Each project is led by a Core staff
member who is responsible for ‘spec’ing the project, making sure the project is completed
on time within budget and then billed. While a staff member manages the project, each
project generally has faculty oversight to ensure the science behind the project is sound.
Internally, we track projects/code with TRAC. We have evaluated many tools for tracking
projects including BaseCamp, dotProject, Drupal extensions, Document Management, Wiki’s,
etc. We built Laboratree to manage documents and messaging. We have built web-based
tools to support other projects on campus, such as the Consortium for Breast Cancer
Pharmacogenetics.
CONTACT INFORMATION