Frequently Asked Questions

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.

Q4: What is Track 1, Track 2 or Track 3 work?
A: Please see explanation in this page.

Q5: Do you analyze PacBio and Oxford Nanopore data?
A: Yes. Due to the fast evolving nature of the Pacific Biosciences (PacBio) and Oxford Nanopore (ONT) technologies, analysis projects involving PacBio or ONT data are always considered Track 3 work. See this page for further discussion.

Q6: Do you do work that is heavily informatics-oriented, e.g., gene and genome annotation?
A: Yes. Informatics- or annotation heavy projects belong to Track 2 work. Click here for explanation of the 3 service tracks, and visit this page for a full list of services that we offer.

Q7: Can you develop a computational pipeline to be executed in our own hands, rather than completing the work directly by your bioinformaticians?
A: Yes, this is considered "software solutions" type of work. Please understand that the standards for developing pipelines to be executed in your hands - in terms of the robustness of the code and documentation - are considerably higher than the ones to be developing pipelines to be run by us directly, thus it will cost considerably more. Visit this page for a full list of services that we offer.

Q8: Can you help us develop databases and web servers?
A: Yes, database and web service developments are categorized as Track 2 work. Visit this page for a full list of services that we offer.

Q9: Are you able to help us do a GWAS (genome-wise association study)?
A: Yes. GWAS is always considered Track 3 work, however, because of the uncertainty involved. See this page for explanation of the 3 service tracks.

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.

Q12: Can you do AI/deep neural network/deep learning developments?
A: Yes, AI/machine learning/deep learning developments are always considered as Track 3 work.

Questions about our capacities and strengths

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.

Q18: We were satisfied with your report and the payment was made. But now, we have got new questions about the work. Can we talk with you again?
A: Yes, we would be happy to talk again and address your new questions.

Q19: Will you help us write grant applications?
A: Please see this page for discussion on this topic.

Q20: Show me some proof that you have successfully completed some bioinformatics projects with other researchers.
A: This page shows a long list of institutions (and other organizations) that we have successfully completed bioinformatics projects with. On your request, we will provide contact info of the individual researchers associated with any of these institutions as references for you to check.

Q21: How have researchers evaluated your work in the past?
A: Check out the testimonials left by researchers who have used our services in the past at this page. All of these researchers have revealed their identities. You are welcome to contact them directly and obtain a more personal evaluation of their experience working with us.

Q22: What other advantages are there for researchers to use your services?
A: See a series of discussions on this topic starting from this page.

Q23: Besides the saving in time and money that you mentioned, are there other differences between using your services and using a local bioinformatician? I do have a local bioinformatics collaborator that is quite capable.
A: A local collaborator could be advantageous if you would prefer to have face-to-face meetings often, though for the types of work we bioinformaticians do, face-to-face meetings are in theory not really required. Other differences between using us and using a local collaborator include: first, when working with us, you are a client of a commercial entity. The standards we abide by while doing the work are arguably higher than ones observed by an academic collaborator - who undoubtedly has other priorities. Second, in contrast to an intricate academic collaboration relationship you have with a bioinformatics collaborator - either local or of a different institution, your relationship with us is clear-cut. For instance, there will never be a dispute about authorships or other tricky things of that type.

Questions about our price

Q24: You have such a brilliant team of bioinformatics experts with dazzling resumes, you must be expensive. Why do you say using your service can lower researchers' cost?
A: Although a highly experienced bioinformatician costs more *per unit time*, when carrying out a project, he/she makes much fewer wrong turns than an inexperienced one does, and ends up costing less time and less money *for a project*. See this page for further discussion on this topic.

Q25: How much will you charge for a project?
A: Projects vary in sizes and complexities. An average-sized project costs about $7,500 to complete.

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.

Q27: How much saving in time and money can I expect if I use your service to complete my bioinformatics work?
A: Projects vary thus there isn't a fixed answer to this question. Summary statistics of a slightly outdated poll suggests that our services lead to ~80% saving in cost and ~65% saving in time. See this page for more details. Note that the benefit of using our services goes beyond what these numbers tell: often times it makes the difference between "not doable" and "doable". Please visit this page for further discussion on this topic.

Q28: What you quoted is beyond our budget. Can you consider a discount?
A: Because we have tried very hard to provide our services at the lowest prices possible - see this page for more discussion on this topic - generally, it would be difficult for us to apply further discount to the quotes we make.

Questions about data

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.

Q30: Is there any chance you will share our data with a third party?
A: Absolutely no.

Q31: Will you sign a non-disclosure agreement (NDA) or a confidential disclosure agreement (CDA) before we conduct a deep discussion the project or send you our data?
A: We will gladly do.

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.

Q37: How many researchers have you helped? And how many projects have you completed? Are they all from the U.S.?
A: In the past six years of our operation, AccuraScience has interacted with 1000+ researchers all over the world and assisted in their project design and implementation, and directly carried out bioinformatics projects for 200+ researchers from 80+ academic institutions, biotech and pharmaceutical industries and government agencies across five continents around the globe. See this page for a partial list of institutions and other organizations that we have worked with.

Miscellaneous questions

Q38: Where is the work actually performed?
A: Most work is performed in our facilities in Johnston, IA. Some work is carried out in our branching office in Beijing, China.

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.

Q40: Are you hiring?
A: Yes. Visit this page for career opportunities at AccuraScience.

Did not find answer to the question you have? send us an inquiry, chat with us online (during our business hours 9-5 Mon-Fri U.S. Central Time), or contact us in these other ways.