Bioinformatics Core (Aim #1 and 2) The specific goals of the MS-INBRE Bioinformatics Core are: 1) build on existing interdisciplinary collaborations; 2) create new collaborative efforts between the PUIs and the research intensive universities; 3) train PUI students in bioinformatics; and 4) help address the serious cyberinfrastructure needs in Mississippi. To reach these goals the bioinformatics core will focus on improving bioinformatics awareness and literacy in Mississippi. The Bioinformatics Core will assist the PUI investigators with their scientific needs (Aim #1). Based on past experience (see Progress Report section for example), we envision that the following services will meet the scientific needs of PUI investigators: 1) Design and implementation of bioinformatics methods needed for projects. Bioinformatics solutions to research questions often require the integration of multiple bioinformatics methods in a computational pipeline. Increasingly, the use on spreadsheets by research investigators and students to manage and analyze results is also not optimal for comprehensive discovery of biological implications from data. The lack of expertise for these types of bioinformatics solutions could limit the research questions pursued and reduce the overall impact of the research project. Likely common small-scale bioinformatics analysis will include sequence and structure and phylogenetic analysis. Extracting information from literature databases is also a need for research projects that the Core can provide expertise. More complex analysis could include gene, protein and metabolite expression. As an example. Dr. Heda, a PUI investigator at MUW, utilized proteomics to study the cystic fibrosis transmembrane conductance regulator (CFTR). This project will generate large amounts of mass-spectrometry datasets in form of ion spectra that must be assigned to peptide sequences as well as inferences on protein abundances. The core will provide training for Dr. Heda and his students on understanding of the data exchange formats associated with mass spectrometry experiments such as mzML, TraML, mzldentML, mzQuantML and PSI-MI XML. 2) Advise on hardware and software needs for data storage, data sharing and data analysis. Types of data input or outputs associated with MS-INBRE projects include images from microscopes, tables of data, graphs, genomic and protein sequences, molecular pathway diagrams, videos of experiments and audio files. The data storage, sharing and analysis needs of MS-INBRE research projects vary depending on the data type. Thus the solution for each project will be customized. A critical need to facilitate research collaboration among MS-INBRE researchers is the implementation of a cyberinfrastructure for seamless and secure storage of data. In some cases, it is desired to have data storage, analysis and sharing to be accessible off-line and via a website. Visual analytics tools are making it possible for these data processes to be done together with minimal computer programming. 3) Contribute to grant proposals. The Bioinformatics Core will help provide preliminary data appropriate for inclusion in grant proposals. This data generation will be done in consultation with the collaborative research investigator. Standard or customized text for inclusion in the grant proposals will also be provided to investigators.
The aim of this effort is to strengthen the research projects by adding the appropriate bioinformatics components. This is particulariy critical for PUI investigators. 4) Other technical services. The Core will provide assistance with the following bioinformatics topics: (1) Genome analysis; (2) Sequence analysis; (3) Phylogenetics; (4) Structural bioinformatics; (5) Gene expression; (6) Genetic and population analysis; (7) Systems biology; (8) Data and text mining; (9) Databases and ontologies and (10) Bioimage Informatics. Bioinformatics Literacy Project (Aim #2). Biomedical research involves the management and analysis of large and complex datasets requiring an understanding of a variety of bioinformatics software and databases. An urgent need identified by the MS-INBRE Bioinformatics Core is the need to build up the expertise of investigators and students at the PUIs in bioinformatics. The Bioinformatics Core has developed several tools that target PUIs. This is a critical need because PUIs do not have significant access or exposure to bioinformatics as an area of study. These tools will contribute to the development ofthe student pipeline into biomedical research. We have developed a Bioinformatics Literacy Project that will begin to address this issue. We believe that full implementation of this project at the PUIs will lead to the training of a large cohort of students in bioinformatics. The training components of this project are: 1) Bioinformatics Test Bank System. In this training infrastructure component, cohorts of trained graduate students at the core director's institution (JSU) read peer-reviewed bioinformatics articles and construct questions along with multiple-choice answers in the bioinformatics research areas. Questions are scored resulting in consensus questions. The Bioinformatics Test Bank system when fully developed will provide a resource for self-directed bioinformatics training, continuing education as well as competency testing. These questions will also be used in the bioinformatics traveling workshops at the PUIs. Ultimately however, the goal ofthe core is to infuse these modules into the science education curricula at the PUIs. 2) Bioinformatics Text Annotation. With a similar goal as above, experienced graduate students will help develop the bioinformatics curriculum by developing tools that facilitate learning. The abstract of a journal article on bioinformatics topics provides concise information about the article. The Sentence Annotation training infrastructure component was implemented to characterize sentences in abstracts by Focus - type of the information conveyed by the statement. Focus dimensions can be classified into three various types: Scientific (S) discussing findings and discovery; Generic (G) stating general knowledge, clarifying the structure ofthe paper, etc.; Methodology (M)describing a procedure or a method. A database of categorized sentences can be a learning resource for understanding bioinformatics facts. We have developed sentence segmentation algorithm, which splits titte and abstracts for sets of citations indexed in PubMed into sentences. Further, a web resource to retrieve the sentences is available based on keyword and PubMed Identifier (http://genomics.jsums.edu/sentence/bioinformj_pubmed/). 3) Short Bioinformatics Research Projects. Short-term (1-6 months) bioinformatics research projects can help students develop specialized bioinformatics skills. The bioinformatics core is coordinating efforts to develop short-term project ts that students (PUI and others) can engage in remotely from their institution with guidance from the core director. A collection of projects will be used for mentored senior year projects as well as objectives for graduate student theses or dissertation. Short-term projects are envisioned to have a mentoring component that may require an initial visit to JSU for training, however student-initiated projects will also be encouraged. We believe that this activity, once fully developed, will become an important resource for students at the PUIs or other institutions who lack faculty with bioinformatics expertise. 4) Bioinformatics Training Workshops. We have designed a training workshop series to provide research-driven level-defined introductory and advanced training workshops for students and faculty in Mississippi. The following workshops have been developed: a. Introductory Bioinformatics I (Introduction, Sequence Analysis, Databases and Ontologies) b. Introductory Bioinformatics II (Genome Analysis, Phylogenetics, and Structural Bioinformatics) c. Advanced Bioinformatics I (Gene Expression, Genetic and Population Analysis) d. Advanced Bioinformatics II (Systems Biology, Data and Text Mining) These traveling workshops will be conducted at the PUIs so that they reach students who otherwise would not be exposed to bioinformatics as a field of study. They will also be used as a tool to advertise the bioinformatics core services to investigators at the PUIs. We also plan to use these traveling workshops to cultivate interdisciplinary collaborations between the PUIs and research-intensive universities.
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