Montana INBRE Bioinformatics Core
What is Bioinformatics?
Bioinformatics is the creation of computational tools to acquire, store, organize, archive, analyze, and visualize biological data—including medical, behavioral, associated environmental and health data. Bioinformatics has a strong overlap with the field of computational biology, which is is the study of biology using computational techniques. While bioinformatics is about software engineering, computational biology is about science. Both are interdisciplinary in nature due to the type of computational tools that are involved, which typically combine methods from computer science (e.g., software engineering, databases, machine learning), mathematics (statistics), and engineering (modeling).
How is Bioinformatics different from Genomics, Transcriptomics, Proteomics, and Metabolomics?
Bioinformatics is a research field while genomics, transcriptomics, proteomics, or metabolomics is the scientific study of a subset of molecular activities in living systems; namely, DNA and their constitutive genes, RNA, amino acid sequences and proteins, and the production of metabolic products and intermediates. Revolutionary advancements in technologies used to generate these types of data result in the accumulation of large, complex sets of information. The management and analysis of this information is not trivial, and typically requires advanced methods developed in bioinformatics - such as alignment of sequences, genome or transcriptome assembly, information retrieval from databases and visualization. Bioinformaticians may also be involved in the early stages of biology projects to provide guidelines for experiment design, data generation and data handling. Indeed, funding agencies are increasingly enforcing proper data management plans for research projects.
Who are Bioinformaticians?
"Bioinformatician" is a general label for biologists with training in computer science, mathematics or engineering - but it also applies to non-biologists using techniques from their respective field to address biology problems. As such, "bioinformatician" covers a broad spectrum of scientists from various fields, all united by their interest in solving biological problems. Note that although "computational biologist" is sometimes used, that title is not as prevalent as bioinformatician.
How can Bioinformatics add to research?
Bioinformaticians contribute to scientific research through active collaboration at all stages of a project. For example, bioinformatics will help investigators design their experiments in order to maximize experimental outcomes, both in terms of data quality and quantity. Bioinformatics will also simultaneously streamline and expand the scope of analyses that an investigator could perform on this data: first, computational tools can be designed (either from existing off-the-shelf solutions, or custom solutions) to process large amounts of information quickly, and look for subtle correlations and patterns in large, multidimensional datasets. Second, sophisticated tools and techniques borrowed from other fields (machine learning, mathematical models, etc.) expand the set of hypothesis an investigator can assess. As such, bioinformatics is about scaling up research projects, both in size and in scope.
What can the Bioinformatics Core specifically help with?
The Bioinformatics Core at Montana State University is a one-stop solution for life science investigators in search of bioinformatics support services and/or computational resources (such as processing power and data storage). We are a team of bioinformaticians with background in molecular biology, biochemistry and genetics providing the following services:
We can help scale your analyses. We are skilled computational biologists; we can help you optimize your experiments to ensure the highest quality and compliance to standards of your results, and suggest alternative approaches to best address your needs. We use advanced high-performance computing techniques to process more data, faster, and in a reproducible way.
We can process data generated by the most recent technologies. We are skilled data scientists; transcriptomics (microarrays, RNA-seq), ChIP-seq, metagenomics, metabolomics datasets are now routinely generated by next-generation sequencing technologies and mass spectrometers, and we have expertise in processing these datasets for you from quality control to hypothesis testing.
We can implement new solutions for you. We are skilled programmers; when existing computational tools are not satisfactory, we can create customized analysis pipelines on the university compute hardware infrastructure.
The Bioinformatics Core also maintains a close collaboration with the Research Computing Group at Montana State University Information Technology Center (ITC), and as such can address your needs for data storage and high-performance computing.
What can the Bioinformatics Core cannot specifically help with?
Bioinformaticians are (usually) not biostatisticians, software engineers, not IT specialists, although they have a large practical experience in these fields. While the Bioinformatics Core can provide comprehensive support in statistics or software development, it cannot substituted actual experts in those fields when a certain level of expertise is needed. Depending of the complexity of the problem at hand, the Bioinformatics Core may consult with these field experts to provide the best service; bioinformaticians will then act as an interface between the investigator and the field expert to ensure the best communication across disciplines.
At what point should I contact you for your Bioinformatic services?
As early as possible in the planning of your research project. While we can usually extract meaningful information from previously collected data—including legacy data, the real benefit of a bioinformatician is to provide input at each stage of a project to maximize the number and complexity of the scientific hypotheses that will be successfully assessed.
What are the additional costs to researchers?
Since its creation in 2009 the Bioinformatics Core has been mostly supported by federal funding through the NIH INBRE, NIH COBRE and NSF EPSCoR programs as an experiment to meet the demand on campus for bioinformatics expertise and services. These services have mostly been offered for free or small fees, and will continue to be so when collaborating on pilot projects. Beyond pilot projects we require investigators to add budget lines for the Bioinformatics Core whenever they apply for a grant. Details of the amount requested depend of the scale and complexity of the project; often a flat fee is requested when standard analyses are involved.
What types of projects has the Bioinformatics Core worked on recently?
Our portfolio of projects covers a wide set of sub-specialties of biology, including but not limited to molecular biology, cellular biology, infectious diseases, ecology, biochemistry, plant and animal science. The Bioinformatics Core has the expertise to process genomics (genome assembly and annotation, metagenomics, comparative genomics, SNP calling, phylogenetics), transcriptomics (microarrays, RNA-seq, metatranscriptomics), proteomics (ChIP-seq) and metabolomics data (mass spectrometry, NMR). We also have expertise in programming, high-performance computing, cloud computing, database development, and web development.
The field of applied bioinformatics is developing at a pace not normally experienced in most biology labs, and the goal of the MT INBRE Bioinformatics Core is to help students and researchers keep up through the promotion of bioinformatics and computational literacy throughout the science curriculum and in the laboratory. This goal is being addressed through three main endeavors: (1) maintaining equipment and software for bioinformatic research, (2) promoting bioinformatics education, and (3) providing training and support to biologists implementing bioinformatics tools in their research. Many of these services are available to students and researchers throughout the Montana INBRE network, and details can found at the Bioinformatics Core Facility website.
CORE FACILITY LINKS
- Bioinformatics Core Facility*
- Functional Genomics Core Facility*
- Proteomics/Mass Spec Core Facility
- NMR Core Facility
- Microscopy Core Facility
- Imagining & Chemical Analysis Laboratory (ICAL)
- UM Remote-Access Electron Microscopy Core Facility*
* INBRE-supported core facilities