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.

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OVERVIEW

RESOURCES

RESEARCH CONTRIBUTION HIGHLIGHT LIST OF SERVICES

QUALITY CONTROL AND ASSURANCES

CONTACT INFORMATION

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.

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/

Preferred Platforms

Platform Linux/Apache/MySQL/PHP – Although we also support sites in Python, Perl, Java and ColdFusion

Framework CakePHP – MVC programming in PHP. Also use Drupal and Joomla.

Workflows Python and/or Perl

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.

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.

Supported Analysis

Proteomics

Microarray

SNP Arrays

Pharmacogenetics/Correlative-Studies

Sequence analysis/next generation sequencing

MetabolomicsMolecular/physiological static/dynamics network modelsText mining

Database access

Custom built tools

• Data Analysis

• Biomedical Data Management

• Graphic/Web Design

• Consulting

• Community & Training

• Tool Access

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.

Service cores in various disciplines are being initiated in medical schools and universities across the country with the intention of serving principal investigators through many services including microarray experiment execution, data analysis, visualization, and software development. We present the development of the Bioinformatics Core at Indiana University School of Medicine, lessons learned, and best practices implemented.

We present example projects with a simple explanation of core operations, and lessons learned in establishing new projects, collaboration, project development, and advertising. We also discuss practices we've adopted in development, analysis, and technology.

The challenge

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.

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.

Bioinformatics Service Core