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

Q1.1: Who are your customers?
A: Our clients include researchers from academic institutions, biotech and pharmaceutical industries, clinical facilities, and government agencies. Eighty-five percent of our clients are from academia. This page shows a partial list of our current client and partner organizations.

Q1.2: What kind of services do you provide?
A: We offer a variety of bioinformatics services, including but not limited to: processing, analyzing, and interpreting high-throughput biological and medical data, with a focus on next-generation sequencing (NGS) data (Illumina, Pacific Biosciences, Oxford Nanopore Technologies), 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. To learn more, see this page.

Q1.3: Are you familiar with single-cell RNA-seq, single-cell ATAC-seq and Multiome data analysis?
A: Yes. See this page for a discussion of our experience in analyzing those data types

Q1.4: Do you analyze data produced using protocols similar to ChIP-seq?
A:Yes, we are familiar with data generated from other experimental protocols measuring chromatin binding by DNA-binding proteins and/or chromatin accessibility, including ATAC-seq, CUT&RUN, CUT&Tag, HiCHIP, and PLAC-seq.Send us an inquiry if you have additional questions.

Q1.5: 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 many NGS applications and data types, and new ones are constantly being developed. It is not possible for us to list them all. However, 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 does not mean that pipelines designed for existing applications/data types will automatically work for your new data - some tuning and tweaking will likely be required. In short, yes, we will help with these new applications and data types.

Q1.6: What is Track 1, Track 2 or Track 3 work?
A: Please see this page.

Q1.7: Do you analyze PacBio and Oxford Nanopore data?
A: Yes, due to the fast-evolving nature of Pacific Biosciences (PacBio) and Oxford Nanopore (ONT) technologies, analysis projects involving PacBio or ONT data are always considered Track 3 work. For further discussion, see this page.

Q1.8: 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. For more information on the three service tracks, click here. A full list of the services we offer can be found on this page.

Q1.9: 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 type of work is considered "software solutions" work. Please note that the standards for developing pipelines to be executed by you, in terms of code robustness and documentation, are higher than those for developing pipelines to be run by us directly. As a result, this work will cost considerably more. A full list of the services we offer can be found on this page.

Q1.10: Can you help us develop databases and web servers?
A: Yes, database and web service development is classified as Track 2 work. For a full list of the services we offer, see this page.

Q1.11: Are you able to help us do a GWAS (genome-wise association study)?
A: Yes, GWAS is always considered Track 3 work due to the uncertainty involved. For more information on the three service tracks, see this page.

Q1.12: I am curious why genome assembly is not listed in Track 1, routine analysis?
A: Although there are established pipelines for genome assembly, each genome assembly project is unique and requires special attention due to project-specific considerations. It is often necessary to test and compare multiple pipelines and/or configurations in order to get the best possible assembly. Therefore, genome assembly projects are always considered Track 3 work. De novo assembly of transcriptomes (using RNA-seq data for a species without a reference genome) and metagenomics projects are also considered Track 3 work for similar reasons. Please note that being classified as Track 3 work does not necessarily mean that these projects will be more costly. If you would like to discuss this further, please contact us.

Q1.13: Can you provide flat-rate quotes for Track 3 work?
A: Track 3 work is research-oriented, and it is difficult to predict beforehand how much effort will be required to complete a research project. Therefore, an hourly rate pricing model may be more appropriate. However, as most researchers do not like open-ended commitments, we try to provide a flat-rate quote if requested. This requires extensive communication with the researcher to arrive at a flat-rate quote.

Q1.14: Can you do AI/deep neural network/deep learning developments?
A: Yes, you can find our discussion on AI/deep learning modeling work on this blog page. With the exception of work involving established and routine methods, most AI/machine learning/deep learning development work is considered Track 3 work.

Q1.15: Can you help us with AlphaFold modeling work or other structural biology/structural bioinformatics work?
A: Yes, you can find our perspective on AlphaFold modeling on this blog page. AlphaFold and other structural bioinformatics work are considered Track 3 work.

Questions about our capacities and strengths

Q2.1: Who are your Lead Bioinformaticians?
A: Our Lead Bioinformaticians are highly experienced and qualified bioinformatics experts. Many of them have 15 to 20 years of experience working in the bioinformatics field, with a long list of publications supporting their credentials and capabilities. You can view their profiles on this page. For more information on their experiences, see this page.

Q2.2: What are some of the unique strengths of your Lead Bioinformaticians?
A: Many of our Lead Bioinformaticians have dual educational backgrounds, such as a Ph.D. in biology and a M.S. in computer science or statistics, as well as several years of postdoctoral experience and experience working as professors or principal investigators in major U.S. institutions. To learn more about why a dual background is important for proficient bioinformatics work, see this page. You can find more information on how the strong expertise of our Lead Bioinformaticians can make the difference between success and failure in challenging bioinformatics projects on this page.

Q2.3: 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 correctly and to the best knowledge of the science community at the time of completion. Track 3 projects, which are research-oriented, involve a high level of uncertainty. We cannot guarantee that our work on a Track 3 project will necessarily be "successful" in the sense of producing the expected results. However, if we are unable to make a Track 3 project "work," it is likely that no one else can. You can find more information on this topic on this page.

Q2.4: Tell me about your experiences in AI/machine learning/deep learning developments.
A: Two of our Lead Bioinformaticians are pioneers in the development of machine learning in bioinformatics. One of them, Dr. Justin Li, was the first researcher to develop SVM regression models in the biological field. This groundbreaking paper, published in 2006 and for which Justin was the senior author, was identified by Thomson Scientific as a "new hot paper" in the field of Computer Science in November-December 2007. Justin has continued to conduct research in machine learning and deep neural network applications and has published around 10 papers in related areas. He is also the author of the blog series "AI Models in Bioinformatics".

Q2.5: Will you help us write manuscripts?
A: We do not typically directly participate in manuscript writing. However, for each project we complete, we provide a report that includes a Methods and Results section, similar to the corresponding sections in research publications. We also assist in addressing critiques raised by reviewers when your manuscript is peer-reviewed. For more information, see this page.

Q2.6: 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 have another conversation and address any new questions you may have

Q2.7: Will you help us write grant applications?
A: For more information on this topic, see this page.

Q2.8: 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) with which we have successfully completed bioinformatics projects. Upon request, we can provide contact information for individual researchers at these institutions as references for you to check.

Q2.9: How have researchers evaluated your work in the past?
A: You can read testimonials from researchers who have used our services in the past on this page. All of these researchers have disclosed their identities. You are welcome to contact them directly to get a more personal evaluation of their experience working with us.

Q2.10: What other advantages are there for researchers to use your services?
A: For more information on this topic, see this page and the subsequent pages in the series.

Q2.11: 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 might be advantageous if you prefer to have frequent face-to-face meetings, although for the type of work that bioinformaticians do, face-to-face meetings are not strictly necessary. Some other differences between using us and a local collaborator include: first, when working with us, you are a client of a commercial entity, and the standards we follow while completing the work are likely higher than those observed by an academic collaborator, who may have other priorities. Second, in contrast to the complex academic collaboration relationship you might have with a local or out-of-town bioinformatics collaborator, your relationship with us is straightforward. For example, there will never be any disputes about authorship or other sensitive issues.

Questions about our price

Q3.1: 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 having a highly experienced bioinformatician may cost more per unit time, they are able to complete projects more efficiently by making fewer wrong turns and ultimately costing less time and money for the project. For more information, see this page.

Q3.2: How much will you charge for a project?
A: The cost of a bioinformatics project depends on its size and complexity. On average, our projects cost around $7,500 to complete. However, the final cost can vary significantly depending on the specific requirements and needs of the project. It is best to contact us to discuss your project in detail and receive a quote.

Q3.3: What work is covered in a $7,500 "project"?
A: The cost of a project can vary greatly depending on its size and complexity. On average, an average-sized project costs about $7,500 to complete. However, it is important to note that the term "project" is not well-defined and can vary in size and complexity. A Track 3 project may involve bioinformatics work with 1-2 data types that produce multiple figures and are suitable for publication in a scientific journal. Some projects may be larger and result in multiple manuscripts being written. It is important to communicate with the bioinformatician to understand the scope and cost of the project before starting work.

Q3.4: How much saving in time and money can I expect if I use your service to complete my bioinformatics work?
A: It's not possible to provide an exact answer to this question as projects vary greatly in size and complexity. However, summary statistics from a slightly outdated poll suggest that our services can result in approximately 80% savings in cost and 65% savings in time compared to alternative options. More information on this topic can be found on this page, which includes details on the benefit of using our services beyond cost and time savings. It's important to note that using our services can often make the difference between a project being "not doable" and "doable." Additional discussion on this topic can be found on this page.

Q3.5: What you quoted is beyond our budget. Can you consider a discount?
A: To provide our services at the lowest prices possible, we have worked hard to ensure that we are efficient and effective in the way we do our work. As a result, it is generally difficult for us to offer further discounts on our quotes. Please see this page for more information. However, we do understand that every project is unique and may have its own specific needs and challenges. If you have any specific concerns or needs for your project, we encourage you to discuss them with us and we will do our best to accommodate them to the best of our ability.

Questions about data

Q4.1: 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.

Q4.2: Is there any chance you will share our data with a third party?
A: Absolutely no.

Q4.3: 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.

Q4.4: Our project involves the using of controlled access data at dbGAP (or TCGA). How should we deal with this?
A: We 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 options for AccuraScience to obtain access to the data. The first option is for us to write a brief proposal, listing the work we will do on your project, and submit it to dbGAP (or TCGA) for approval. The second option is for you to write a brief proposal, listing AccuraScience's personnel as a "collaborator" in your proposal, and submit it for approval. Either way is acceptable to us.

Q4.5: How safe are our data in your hands?
A: The security and safety of our clients' data is our top priority. Our data center is located in a physically secure location, protected by professional security services 24 hours a day. We only put data online when absolutely necessary, and our server computers are professionally managed with all current security features deployed. If you have special needs for handling your data, please let us know.

Q4.6: 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 on any human data prior to transferring it to AccuraScience's facilities. It is the client's responsibility to fully comply with the Health Insurance Portability and Accountability Act (HIPAA) and other laws and regulations of the United States or any other applicable countries when collecting and transferring human data to AccuraScience. AccuraScience is not responsible for any compliance issues on the part of the client, whether intentional or unintentional.

Questions about the company

Q5.1: When did AccuraScience get started, and by whom?
A: AccuraScience was founded in 2013 by a team of professional bioinformaticians, bioinformatics software developers, and investors with a combination of strong expertise in academic research, industrial development, and business operations.

Q5.2: How did you come up with the idea of starting this operation?
A: In summary, AccuraScience was founded to address the challenges faced by researchers in obtaining reliable and cost-effective bioinformatics support. Our team of experienced bioinformaticians can provide high-quality data analysis services at a lower cost than hiring a local bioinformatician, and our business operation ensures that we adhere to high standards in our work. We offer a range of services to meet the diverse needs of researchers, and our team has a strong track record of success in helping researchers achieve their goals. For more information about the benefits of working with AccuraScience, please see this page.

Q5.3: How many researchers have you helped? And how many projects have you completed? Are they all from the U.S.?
A: AccuraScience has had extensive experience working with researchers from various institutions and organizations across the globe. In the past six years of operation, we have interacted with over 1000 researchers and directly carried out bioinformatics projects for more than 200 researchers from over 80 academic institutions, biotech and pharmaceutical industries, and government agencies on five continents. You can view a partial list of the institutions and organizations we have worked with on this page.

Miscellaneous questions

Q6.1: Where is the work actually performed?
A: Our facility is located in Johnston, IA, United States, where all of our work is carried out.

Q6.2: What computational infrastructures do you have?
A: Our state-of-the-art facility in Johnston, IA, United States is equipped with high-performance computers featuring a total of 600+ cores, 15TB of RAM, and 2 PB of redundant disk space. We have the ability to utilize public clouds such as Amazon Web Services (AWS) and Google Cloud Platform (GCP) for projects that require additional resources.

Q6.3: Are you hiring?
A: Yes. Visit this page for career opportunities at AccuraScience.

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