what we do
We help our clients solve their scientific research and development problems through the application of computing.
Data by itself is not knowledge, but rather its true value is only unlocked when there are suitable intellectual frameworks within which it can be structured, organized and reasoned with. Most of our clients have no lack of data, but they do often need help transforming that data into the kind of actionable insight that can advance a research and development program - and that’s where we come in.
Working at the intersection of science and computation, we help our clients transform data into insight through the application of computational approaches ranging from the development of custom algorithms and software for exploring their research data in new ways, to the advanced, causal modeling and simulation of the complex systems that they are studying in the lab.
As scientists and researchers ourselves, our understanding of the challenging, iterative, and nonlinear nature of research and development has been gained from decades of experience solving real-world research problems in academic and commercial environments ranging from universities and medical schools to small venture capital-funded startups and global pharmaceutical companies.
Our clients include major research universities on both U.S. coasts, and commercial life science companies based in the U.S. and in Europe. We are also a contractor on the NASA Transiting Exoplanet Survey Satellite (TESS) mission that was launched from Cape Canaveral in early 2018.
Amber Biology is based in Cambridge Massachusetts, USA.
partners
Alex Lancaster is an evolutionary biologist, engineer, writer and Partner at Amber Biology. Alex completed his Ph.D. in evolutionary biology at the University of California, Berkeley, and also holds bachelor's degrees in physics and electrical engineering. He has worked in research & development in both Australia and the United States with a major focus on evolutionary and systems biology. He has also worked extensively in genomics, analyzing next-generation sequencing data and has developed tools for clinical and population genomics, with a particular specialization in immunogenetic applications. He has held research and faculty positions in academia, as well as R&D positions in the broadcasting and IT industries.
Alex has published many peer-reviewed papers and is interested in solving problems in biology using evolutionary and complex adaptive systems approaches. He has done pioneering work in this area as a co-developer of the open-source agent-based modeling toolkit, Swarm, one of the first tools for large-scale modeling of collective behavior in biology and beyond. He is passionate about the power of open source and open science approaches to accelerate discovery.
After completing a PhD in biophysics and structural biology at the University of London, Gordon has worked in life science R&D in both Europe and the U.S., with a particular emphasis on molecular engineering and computational biology. In academic and commercial environments ranging from universities and medical schools to small venture capital-funded startups and global pharmaceutical companies, he has served in a diversity of roles from research faculty to company vice president.
Gordon is the author of numerous original scientific articles and patents and has created and managed some very successful research partnerships with industrial, academic and government organizations. He initiated and managed the first translational oncology clinical trial at a multinational pharmaceutical company and has coached and led research project teams in large matrix organizations, as well as large, distributed teams of scientists. software developers and technical specialists, working together across multiple time zones.
Gordon’s career path has always reflected his belief that the most interesting and potentially promising areas of research lie at the intersections between the traditional scientific disciplines.
Consultants
Our network of life science and computer science specialists includes some wonderfully talented independent contractors to whom we turn for their expertise and advice on some of our projects.
Molly grew up exploring the natural world, which ultimately piqued her interest in the biological sciences. She completed her Bachelor of Science in biology with a genetics minor at the University of New Hampshire and subsequently earned her Master of Science in biological sciences at the University of Massachusetts Lowell.
During her studies, Molly taught biology and genomics laboratory courses to undergraduate and graduate students. Her research utilizes comparative genomics, leveraging both next-generation sequencing data and bioinformatics.
Molly works a a graduate research assistant, and spends her free time caring for her two guinea pigs and growing her houseplant collection.
Ruth Duerr is a generalist with interests in nearly everything from music and art to science, data, and policy with stops for many other things along the way. She has been actively involved in Earth, space and the information and data sciences for many years.
Her research interests include nearly all facets of science data management, digital archives, records management, digital library science, and software and system engineering. She has actively participated in the Earth and space sciences informatics community, and authored and co-authored many publications on the management and curation of Earth science data.
Ruth has also held leadership positions in groups such as the NASA Earth Observing System’s Operations Working Group, the Research Data Alliance’s e-Preservation Interest Group and Domain Repositories Interest Group, the American Geophysical Union and Earth Science Information Partners (ESIP).
Anabell is a Boston native who grew up loving science. Her passion for learning and building things led her to graduate with a Computer Engineering degree from Northeastern University. After working in industry for five years at Procter and Gamble, as a Manufacturing Engineer, she decided to quit her job and learn Python. After backpacking for a few months around the globe, she spent two months on a beach in Costa Rica learning Python at a bootcamp. She loved Python so much that she returned as a TA for another two months. Through this experience, she learned the versatility of Python and strives to help new learners quickly come up to speed.
Anabell works for an early stage startup as an applications engineer. She spends her spare time with her young daughter and husband, taking photos, or teaching Python.
Gadi Oren is a product person, entrepreneur, engineer and technologist. Gadi completed his MS in management and systems (SDM) at Massachusetts Institute of Technology, Cambridge, and also holds a bachelor’s degree in computer science and electrical engineering. He has worked in various product leadership and strategy roles and took multiple large scale products from a concept stage all the way to the market in areas of communication, IT service management, networking, synthetic biology, and bioinformatics. He also founded two technology start-ups in the areas of IT service management and AI/ML.
Gadi works as the director of product management and strategy at a cloud services company. He is passionate about addressing real-life customer problems with a new approach and the right technology, building a team and a company, and efficiently delivering these solutions.
our extended network of specialists
We often undertake projects that are essentially digital biology at their core, but that also require other specialist skills in addition to our own, and/or additional personnel. For these projects, in addition to the consultants listed above, we draw upon our extensive network of specialists in areas that include cloud computing, databases, programming, information technology, teaching, and data science - as well as other life science specialties. In addition to supporting independent consultants and contractors like ourselves, this enables us to offer our clients an effective matrix approach to their R&D projects, in which we work with our own network of consultants and contractors who are specialists in their respective areas. By hiring personnel with the appropriate skills onto a project as needed, we can assemble an efficient, flexible and cost-effective team that is most responsive to the needs of the project. With certifications in Agile project management and Agile product development, we also possess in-house, the necessary skills, training and experience for the planning and execution of complex projects.
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