Bioinformatics Tools + Analysis
Bioinformatics Tools + Analysis
Biomedical research generates high volumes of complex and sophisticated data. Successful efforts to produce new therapeutics and diagnostics require informed use of this data from public and proprietary sources. To this end, our bioinformatics and science analysis team provides expertise in the tools and brings a deep knowledge of the data and data sources. We mentor, advise, and collaborate with our clients throughout the entire research and development process, from lab automation and assay design to data management, analysis and visualization.
5AM is a bioinformatics partner to our clients, demonstrating rapid turnaround on analysis and bioinformatics tool or software development to keep up with the pace of scientific development. 5AM offers real solutions and values true collaboration and effective communication in both software and science. Whether your goal is to generate reliable analysis results from a single experiment for a paper or to develop an analysis pipeline capable of high-volume automated analysis, 5AM is your partner in navigating the bioinformatics tools and genomic databases you will need to ensure success.
Our clients include the National Cancer Institute and many other pharmaceutical, diagnostic and biotechnology companies. Below is a sampling of nonexclusive solutions we provide.
Selected Bioinformatics and Science Analysis Services
Assay Development
Many research or diagnostic product development projects involve the design of nucleic acid assays. Technologies such as microarrays and next-generation DNA sequencing allow the efficient and cost-effective assay of large numbers of DNA or RNA molecules. The Bioinformatics and Science Analysis team’s deep assay development experience can help you generate high quality and validated assays and produce reusable systems to support future efforts.
Data Integration
The world of pharmaceutical and diagnostic development benefits from the deluge of publicly-available data, both in genomic data sets and in the published literature. Using this data requires expertise in the tools and databases that already exist. Data sources such as PubMed, Genbank®, dbGaP (a database of genetic association study results), dbSNP (a database of DNA sequence variants), and Ensembl form an incredibly powerful, but loosely coupled, framework. 5AM is skilled in making use of such disparate resources and integrating them with our clients’ internal data. We’ll help you identify what matters, and how to find it and use it to expand your understanding.
Biomarker Discovery
Taking high volume data such as microarray results and mining them for significant markers for a given disease or condition is a challenging task. Care must be taken to avoid artifacts and to identify the meaningful signal from the noise. Identifying a smaller collection that is useful as a diagnostic involves such steps as normalization, feature reduction, and predictive model construction. Such models must be properly tested using either cross-validation or independent training and test sets. 5AM uses tools such as R and Matlab for analyzing biomarker data and uses good engineering techniques to build reusable software to meet our partners’ ongoing needs.
Laboratory Workflow and Data Management
Those familiar with the tracking and analysis of laboratory information know that many experiments start small and are tracked in lab notebooks and spreadsheets, but successful experiments often grow much larger and require better tools and data repositories to handle complex and massive datasets. Everything from reliable sample tracking to experiment quality control to data analysis are critical to generating valid results. Laboratory Information Management Systems (LIMS) are typically complex and often require extensive customization. 5AM is skilled in working with lab scientists to understand their needs and understand what level of software and analytical support are appropriate for each project.
Experience and Approach
5AM’s Science and Analysis team has a wide range of capabilities and experience. We draw on over 25 years of combined experience in high-throughput and complex scientific efforts, such as the Human Genome Project. We apply software engineering principles to complex bioinformatics work, which results in transparent progress and rapid results for our clients’ needs.
A wide variety of tools, both commercial and open source, are available for analyzing and mining biological data. 5AM has expertise across this spectrum. We are skilled in R, BioConductor, Perl, Matlab, Python, Java and Spotfire, among others. We use tools such as BLAST, HMMER, Bowtie, Primer3 (and more), and know when to use existing tools – open source, commercial, home-grown – and when to develop custom ones.
Got science? Need solutions?
If you need an advisor or a bioinformatics team for analysis, guidance, or tools, click the link below. Use our deep expertise and flexible approach to further your reach.
