Note: This page was prepared for academic customers. Clients from the biotech / pharmaceutical / therapeutic / molecular diagnosis industries, please visit this web site instead.
Questions about our services
Q1: Who are your customers? A: Our clients include researchers in academic institutions, biotech and pharmaceutical industries, clinical facilities and government agencies. Eighty-five percent of our existing clients are from the academia. This page shows a partial list of our current client and partner organizations.
Q2: What kind of services do you provide? A: We carry out many types of bioinformatics
work, including but not limited to: processing, analyzing and interpreting
high-throughput biological and medical data - with emphasis on
next-generation sequencing (NGS) data (Illumina-, Pacific Biosciences (PacBio)- and/or Oxford Nanopore Technologies (ONT)-based), statistical data analysis, data
integration for diverse types of biomedical and other data, statistical
modeling, data mining, customized and advanced analysis method development,
specific data structure and algorithm development, informatics, database
development, web service development, software solutions, and IT and
infrastructure development. See this page to learn more.
Q3: We need help with NGS data analysis and interpretation, but our data/applications are not on your list. Will you help us? A: There are numerous NGS applications and data types, and new ones keep getting conceived and developed. It is not possible for us to list them all. The good news is, as far as data processing and analysis are concerned, these new applications and data types do not differ substantially from established ones such as resequencing, RNA-seq and ChIP-seq. This is not to say, however, that pipelines designed for existing applications/data types will automatically work for your new data - some tuning and twisting will likely be required. In short - yes, we will help.
Q10: I am curious why genome assembly is not listed in Track 1, routine analysis? A: Although there are established pipelines for genome assembly, our experience is, each genome assembly project is different from all others, and there always are project-specific considerations that require special attention. Moreover, to get the best possible assembly, it is often necessary to test and compare multiple pipelines and/or configurations. Thus genome assembly projects are always considered Track 3 work. For similar reasons, de novo assembly of transcriptomes (with RNA-seq data, for a species for which a reference genome is unavailable) and metagenomics projects are also always considered as Track 3 work. Note, however, categorizing them as Track 3 work does not necessarily mean that they will be more costly. Please contact us to discuss more.
Q11: How are you able to provide flat-rate quotes for Track 3 work? A: Track 3 work is research-oriented work. By its very nature, it is very difficult to predict before-hand how much effort it will take to complete a research project, thus an hourly rate pricing model would probably be more appropriate to apply. However, because most researchers do not like open-ended commitments, we try to come up with a flat-rate quote if this is what the researcher would like to have. It is difficult to do, and it takes extensive communication with the researcher before we are able to arrive at a flat-rate quote.
Q13: Who are your Lead Bioinformaticians? A: Our Lead Bioinformaticians are highly experienced bioinformatics experts. Many of them have between 15 and 20 years experience working in the bioinformatics domain, with a long list of publications supporting their credentials and capacities. Please view their profiles at this page. See further discussion on their experiences at this page.
Q14: What are some of the unique strengths of your Lead Bioinformaticians? A: Most of our Lead Bioinformaticians have dual educational background - e.g., a Ph.D. in biology and a M.S. in computer science or statistics, several years of postdoc experience, and a number of years of experience working as professors or principal investigators (PIs) in major U.S. insitutions. See further discussion on why a dual background is important for proficient bioinformatics work at this page, and how the strong expertise possessed by our Lead Bioinformaticians makes the difference between success and failure in a challenging bioinformatics at this page.
Q15: What guarantee do you have on the services you provide? A: For Track 1 and Track 2 work, we
guarantee that all work is performed properly and correctly, to the best
knowledge possessed by the science community at the time the work is
performed. Track 3 projects involve high level of uncertainty due to their
research-oriented nature. We cannot guarantee that our work on a Track 3
project will necessarily be "successful" in the sense that it will lead to
the results the researcher expects - and often times it is hard to even
specify before-hand what the expected results are. What we can say is that
if we can't make a Track 3 project "work", chances are no one else
can. See further discussion on this topic at this page.
Q16: Tell me about your experiences in AI/machine learning/deep learning developments. A: Two of our Lead Bioinformaticians are among the pioneers in machine learning developments in bioinformatics. In fact, one of them (Dr. Justin Li) was the first researcher to develop SVM regression models in the biological problem domain. This ground-breaking paper published in 2006 - which Justin was the senior author of - was identified by Thomson Scientific (Essential Scientific Indicators, ESI) as a "new hot paper" in the field of Computer Science in November-December 2007. Justin has continued to conducted research in machine learning/deep neural network applications, and has published ~10 papers in related domains. He is also the author of the blog series "AI Models in Bioinformatics".
Q17: Will you help us write manuscripts? A: We generally do not directly participate in manuscript writing. However, for each project completed by us, we deliver a report that includes a Methods and Results section, very much like the corresponding sections in research publications. We also assist in addressing critiques raised by reviewers when your manuscript is peer-reviewed. See this page for further explanation.
Q26: What work is covered in a $7,500 "project"? A: It is true that the term "project" isn't very well defined... To give you a sense of what to expect, an average Track 3 project might cover all bioinformatics work involving 1-2 data types that would produce multiple figures, which, combined with other data, would be adequate for preparing a manuscript with a significant bioinformatics component to be published in a decent scientific journal. A small portion of projects we have completed were of much larger sizes and resulted in multiple manuscripts being written.
Q29: What data format will you accept? A: For most NGS data, we prefer FASTQ format. For non-NGS data, we accept formats commonly used in the field. Generally, we can work with any data format as long as the rules by which the information is encoded are stated.
Q32: Our project involves the using of controlled access data at dbGAP (or TCGA). How should we deal with this? A: We do have access to some dbGAP (and TCGA) datasets for existing projects. But that access cannot be transferred to a different project. For your project, there are two ways for AccuraScience to obtain the access to the data. The first way is for us to write a brief proposal, listing the work we are to do on your project, and submit it to dbGAP (or TCGA) for approval. The second way is for you to write a brief proposal instead, listing AccuraScience's personnel as a "collaborator" in your proposal, and submit it for approval. Either way will work fine with us.
Q33: How safe are our data in your hands? A: The safety and security of our clients' data are our top priority. Our data center is located in a physically secured location and is under protection by professional security services 24 hours a day. The data are not put online unless absolutely necessary, and our server computers are professionally managed with all current security features deployed. Let us know if you have special needs in handling your data.
Q34: What policy do you have on the handling of sequencing data collected from human subjects? A: AccuraScience is only able to handle de-identified human data, but not Protected Health Information (PHI) data. It is AccuraScience’s policy that de-identification must be performed for any human data prior to being transferred to AccuraScience's facilities. It is the client's responsibility to be fully compliant with the Health Insurance Portability and Accountability Act (HIPAA) and other laws and regulations of the United States, and/or of other countries if applicable, when human data are collected and transferred to AccuraScience. AccuraScience is not responsible for any incompliance by the client, intentional or unintentional
Questions about the company
Q35: When did AccuraScience get started, and by whom? A: AccuraScience LLC was established in 2013 by a group of professional bioinformaticians, bioinformatics software developers and investors, with a mix of strong expertise in academic research, industrial development and business operation.
Q36: How did you come up with the idea of starting this operation? A: In brief, while the research community
embraces the tremendous benefit provided by NGS and other new technologies,
they are often handicapped by the shortage of supply in data analysis
capabilities. Hiring a local bioinformatician is expensive, and it is no
secret that junior bioinformaticians (including those newly trained PhDs)
are often not up to the challenges faced day-to-day by cutting-edge
researchers - see further discussion on this topic at this page. Collaboration with a bioinformatician in the academia is not
always easy to establish, and arguably, academic collaboration has its
downsides, because your collaborator always has his/her own priorities. With
these observations, we started AccuraScience as a business operation. With a
cluster of strong bioinformatics experts, we can help many researchers meet
their bioinformatics needs, at a small fraction of the cost required to hire
a local bioinformatician, in the mean time substantially speed up the
execution of their projects - see further discussion at this page. Moreover, as a business operation, we abide by
higher standards than does an academic collaborator. See this page for how AccuraScience was established, and the vision of the people running it.
Q39: What computational infrastructures do you have? A: Our facility is home to an array of high-performance computers with a total of 320+ cores, 2TB of RAM, and 1 PB of redundant disk space. We will make use of public clouds such as Amazon Web Services (AWS) and Google Cloud Platform (GCP) when projects require.