Do well by doing good
Our Philosophy
Boulder BioComputing, Inc. was founded with a particular philosophy for doing science and running a company: do well by doing good. We are motivated by the prospect of doing work that advances the causes of human health and improved therapies. The BBC crew have all worked in the pharma and molecular diagnostics industries, and through these experiences, we have practical perspectives on what it takes to invent drugs and bring products to the markets.
This philosophy benefits our customers by leading our work to be objective and scientifically based – our only goal is to help you, our customer, bring your drug, therapy, or diagnostic to the market more quickly for the service and benefit of human health.
Who we are
Boulder BioComputing, Inc. (originally named "Boulder BioConsulting, Inc.") was founded in Boulder, Colorado in 2013 out of a specific customer need. We started the company to help a former co-worker and friend with a particular scientific computing infrastructure need, only to discover that those needs abound.
Since our founding in 2013, we have grown into a boutique scientific computing, bioinformatics, and scientific consulting company specializing in hard problems that don’t have commoditized answers. If you are looking for someone to take a set of raw sequences, alignment them, and return a .BAM file, we will be happy to help you find a good consulting company. However, if you have a pile of sequence, chemistry, cell line sensitivity, etc. data and want to know the best path to the clinic for your therapy, or if you are a mid-stage pharmaceutical company trying to interpret complex biomarker data to define your next clinical trial, or if you have a mound of legacy scientific and clinical software systems and need a coherent strategy for an overhaul, you have come to the right place.
We begin with a brief call to understand what you are looking for and assess if we can best help you. If we can’t help you or if your needs can be better filled by more commodity consulting, we will tell you quickly; a key tenet of our philosophy is to be as direct, honest, and efficient as possible. Thereafter, we will work with you to set and manage the scope of your project. Each company, each project, and each experiment is unique, but they all are addressed with a focus on practical, biologically meaningful solutions to problems.
Our people
- Broadly knowledgeable in scientific computing and bioinformatics systems, including most R&DIS systems ranging from target identification through lead discovery/optimization and into Phase 2 clinical trials.
- Extenstively experienced with the practical application of most bioinformatics tools, particularly in the context of new target identification and biomarker discovery. Particular focus and experience with oncology-related problems and tools (e.g. CCLE, TCGA, caBioPortal, etc.).
- Recognized leader in R&DIS strategy and management, including all activities from needs assessment and gap analysis, project roadmap and strategy planning, recruitment and hiring planning, budget and justification creation and defense, management mentoring and development.
- Expert in the application of TIBCO Spotfire® to the life science research space – a dyed-in-the-wool data junkie.
14+ years of direct experience running all aspects of pharmaceutical drug discovery, drug development, clinical trial informatics and translational medicine. - 25+ years of experience in software development and project management, primarily for life science industries.
- Systems engineering and architecture.
- Research and Development IT – domain and systems knowledge of systems that support pharmaceutical R&D, from chemical library generation, lead discovery, lead optimization, pre-clinical develop. Implemented numerous solutions from Dotmatics and PerkinElmer.
- Clinical and Translational ID – domain and systems knowledge of systems that support GxP studies, regulatory filings, clinical trial planning and operations (EDC, CDMW, CTMS, site management, payments, targeted SDV, clinical supply fulfillment, etc.). Extensive Medidata and Veeva system knowledge through implementing and configuring numerous solutions.
- Research and Development IT – domain and systems knowledge of systems that support pharmaceutical R&D, from chemical library generation, lead discovery, lead optimization, pre-clinical develop. Implemented numerous solutions from Dotmatics, CDD, Benchling, and PerkinElmer.
- Founder of L7 Informatics and architect of world-class, market-leading product solutions in the LIMS domain.
- Expert in high-performance computing and application of massively parallel technologies to optimize bioinformatics throughput.
- Extensive experience leading life-science systems change to biotech organizations of all sizes.
- 20+ years of leading scientists and software engineers to solve some of the world’s hardest problems in drug discovery and diagnostics development.
· 20+ years of experience in High-Performance Computing, Scientific Software Development, Math-Bio research, Bioinformatics Tool and Algorithm Design.
· Enjoy working at the intersection of Biology, Physics, Mathematics, Computer Science, Bioinformatics, Machine learning and Statistics
· Expert in SUDOKU, FUTOSHIKI and Rubik’s Cube
· Expertise in modern, cross-platform software development and deployment. Delivering turn-key software solutions to research teams worldwide and supporting – data scientists, physicists, biologists and bioinformaticians.
· Expert in building high-performance distributed and parallel systems (including GPU-based software modules)
· Expertise in handling, mining and analyzing large data sets.
· Developed multiple system models to optimize biotech workflows
· 40+ publications
- Cheminformatics, Molecular Modeling, Computational Chemistry – 15+ years experience in the pharmaceutical industry working in all phases of therapeutic drug design – analysis of high throughput screening data, virtual screening, lead optimization in collaboration with medicinal chemistry; techniques include molecular docking, pharmacophore analysis, structure- and ligand-based drug design.
- Bioinformatics, Proteomics – 10+ years experience in bioinformatics including gene expression analysis, analysis of DNA sequencing data and development of DNA sequence analysis pipelines, analysis of proteomics data from clinical and research samples.
- Statistical Analysis, Machine Learning – 10+ years experience applying techniques from statistical learning and machine learning to problems in chemistry, pharmaceuticals and biotechnology; experience with classical statistical methods (regression, classification, survival analysis) as well as method in machine learning including deep neural networks, ensemble methods, and developing novel approaches for data analysis; experience in development, validation, and deployment of predictive models.
Krysta Engel is a PhD molecular biologist and computational biologist with 10+ years of experience analyzing, integrating, and extracting biological meaning from numerous NGS data types. Her informatics capabilities range from raw data wrangling and preprocessing to manuscript quality visualizations and interpretations.
Whether it’s bulk or single cell gene expression, chromatin profiling, transcription factor binding, RNA modification and processing, or genetic variation you’re interested in, she’s got you covered! Krysta has a love for gene expression regulation and understanding how it’s altered across cell types and disease states. She studied these pathways in numerous species both at the bench and with analysis of large omics datasets. Scientific communication, experimental design, and hypothesis generation (e.g. in the form of grant writing), is another passion of hers. Krysta has sculpted her skillset with the intention of being a well-rounded scientist, capable of providing feedback and critical thought at any point of a project.
Bioinformatics:
- Extensive experience running existing analysis tools and pipelines to quantify and analyze sequencing experiments targeting the full spectrum of the central dogma of biology. (gene expression, genetic and epigenetic variation, binding assays such as CLIP-seq and ChIP-seq, etc)
- Advanced publication quality statistics and visualization of data
Multi-omics integration and predictive modeling
Experimental Design, Interpretation, and Communication:
- Deep understanding of experimental design considerations including best practices, technical caveats, limitations, assumptions, and alternative approaches in the areas of molecular biology and genetics
- Technical writing skills including research publications, government and foundation grant and proposal writing and proposal design expertise
- Over 20 years of experience as a bioinformatics scientist and leader with an extensive inter-disciplinary background in NGS and microarray-based genomics and transcriptomics data.
- Strong background in genomics, proteomics and transcriptomics analysis methods, inferential statistics, supervised and unsupervised statistical learning methods, hierarchical data modelling and epidemiological data modelling
Aimee is BBC’s ace administrative person, who keep the company running smoothly.
Interested in joining our team?
Go to careers