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What BioinfoTools offers

Learn about BioinfoTools’ consulting, training, software development and tools

Choosing a consultant

If you’re looking for a bioinformatics consultant or computational biologist, consider these suggestions

Contacting BioinfoTools & FAQ

Feel free to ask about your project (there is no charge for initial queries). The frequently asked questions (FAQ) is available here too.


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Contact
FAQ

Contacting BioinfoTools & frequently asked questions

Contacting BioinfoTools

Enquiries are welcome. Customers are encouraged to use the enquiry form. If you prefer to email directly, please use the appropriate email address below. Your email address will not be given to any other source without your permission. All correspondence will be treated as confidential.

Problems with the web site or comments about its design (positive or negative) should be sent to the webmaster: webmaster@bioinfotools.com

All other enquiries should be addressed to: enquiries@bioinfotools.com

For those requiring a street address to send items by courier, the PO Box listed will accept NZPost courier parcels and will hold larger items. Those wishing to use international courier should first make contact by email or telephone.

BioinfoTools is based in Dunedin near New Zealand’s oldest university, the University of Otago.

FAQ (Frequently Asked Questions)

Contents

General

Copyright and Disclaimer

Introduction

Who are BioinfoTools’ intended clientele?

Can work be done at the client’s location?

Is end-user support available?

Will BioinfoTools develop software on request?

What experience does BionfoTools have?

Software development

What kind of bioinformatics software does BioinfoTools develop?

What areas of biology do BioinfoTools’ software target?

What platforms does BioinfoTools develop for?

Quality control

Will customers be informed of weaknesses?

How are projects or software tested?

Will BioinfoTools guarrantee the performance its software?

Licensing

General

Copyright and Disclaimer

You are welcome to print copies of this or other pages of this website for private use, and to link to them from your own pages. If you want to copy the content, please ask first.

The information on this web site is offered without warranty of any kind. BioinfoTools will endeavour to met the strategies and policies outlined on this website, but reserves the right to vary from them. Readers are welcome to offer comments or corrections; these may be emailed to webmaster@bioinfotools.com

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Introduction

BioinfoTools started life as a software development house, developing core software intended for use by bioinformatics teams in larger companies or research groups. While it retains elements of these roots, most jobs are now computational biology consulting.

BioinfoTools is a vehicle to deliver Dr. Jacobs’ expertise in computational biology. A key strength is a deep background in molecular biology, genetics, as well as computer science and computing.

This biological background goes beyond genomes to include protein sequence and structure work, and is reflected in Dr. Jacobs’ personal research interests in epigenetics, chromatin and genome structure (in both linear and three-dimensional senses), which blend genomics, evolutionary and structural computational biology.

One feature of this background is working on both sequence and structural data, which can add considerable depth to projects.

This strong biological background is also reflected in aiming to draw directly from client’s biological aims and take responsibility for examining the computational opportunities, implementing these and delivering the biological results back to the client.

In the computer science aspects, there is a strong interest in better algorithms for sequence and structure analysis. Of computing technology, there is practical experience in a wide range of programming languages and tools. Details of these are listed below and in the What BioinfoTools offers page.

BioinfoTools aims to assist customers to develop their own bioinformatics strategy. It is an important aspect: “blindly” applying “stock” analysis is never a substitute for understanding the biological issues at hand and then carefully addressing these.

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Who are BioinfoTools’ intended clientele?

Companies and academic research groups of any size.

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Can work be done at the client’s location?

Yes, off-site work is possible by negotiation.

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Is end-user support available?

Yes.

This can take the form of training, documentation, literature reviews, consulting or software development, and so forth, as suits the needs of the work.

For routine tasks, training is likely to be the most effective option. Specialist tasks are best taken in the form of outsourced consulting.

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Will BioinfoTools develop software on request?

Certainly.

Requests may cover any area of bioinformatics, but, in general, requests are best allied to Dr. Jacobs’ background expertise. Briefly, these include:
   • genomics, in particular - epigenetics, chromatin and 3-D structures of genomes
   • protein-DNA and protein-RNA interactions
   • analysis of protein sequence/structure families
   • protein-sequence structure matching
   • protein structural genomics
   • protein structure analysis

Topics outside these areas will be considered but may require additional research time.

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What experience does BionfoTools have?

Dr. Jacobs has extensive experience as an computational biologist. His training includes an undergraduate degree in both computer science and biology (BSc.Hons, First Class; 1982-1986), a doctorate in computational biology (MRC Laboratory of Molecular Biology, Cambridge, England; 1988-1992), five years research experience as a bioinformatics scientist (University of Otago, New Zealand), followed by ten years experience as a consultant.

A brief résumé is available on the About page.

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Software development

What kind of bioinformatics software does BioinfoTools develop?

BioinfoTools retains a software development aspect, both development on request and in-house projects.

In-house, where time permits, exploration of compact and fast storage of sequence and 3-D structure data, sequence assembly, multiple sequence alignment and 3-D structure analysis is undertaken. The biological focus for these are analyses of genomes, in a full epigenetic, chromatin and genome 3-D structure context.

These are aimed to provide cutting-edge bioinformatics solutions to specific bioinformatics problems as discussed in the FAQ What areas of biology do BioinfoTools’ software target?

If you have an interest in these, feel free to discuss them using the contact information at the top of this page. Likewise, you are welcome to discuss development of software to suit your needs.

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What areas of biology does BioinfoTools’ software target?

The answer needs to separately address general-purpose data storage and algorithms for particular uses.

Data storage solutions tend to try be general-purpose to better adapt to later re-use. By contrast, algorithms to tackle a biological question need to be based on a deep understanding of the specific biology tackled and of what algorithmic methods that might be applied while providing a sound biological model.

Broadly speaking, good computational algorithms draw on “first principles” biology. They are best developed by workers familiar with the relevant theoretical biology and experience in the particular area they are to be applied. (The business world tends to refer to this as ‘domain knowledge’.)

Those outside of computational biology (or bioinformatics, if you prefer) may not fully appreciate the extent that it is a large field with niche areas of expertise, just as other areas of biology have. Dr. Jacobs’ background is broader than most. His current biological interests are allied to epigenetics, chromatin structure and genome 3-D structure and, more broadly, structural biology (e.g. the structure and function of DNA, RNA and proteins and their interactions).

Areas of interest in algorithm development are more general, as methods can be applied to different data types, including for example better approaches work with very large amounts of sequence data, genome assembly, multiple sequence alignment, and so on, but are seen as applying within the biological interests listed in the previous paragraph.

Some of the work described involves three-dimensional structures. The biological background and algorithms for this area are not usually found in the those working on sequence data only. A deeper understanding of sequence data and biological systems can be gained by complementing sequence studies with structural biology, with it’s biophysical roots.

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What platforms does BioinfoTools develop for?

BioinfoTools primarily develops software for Unix and Unix-related operating systems (eg. Linux, Mac OS X and commercial Unix platforms), including solutions hosted on an Unix-based server and accessed from any client platform (Mac OS, Windows, Unix-based). This choice of primary target platforms reflects that scientific computing remains dominantly based on Unix-based platforms.

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Quality control

Will customers be informed of weaknesses?

Yes.

All methodologies have strengths and weaknesses; computational biology methods are no exception to this. If a product or project has a known weakness or is unsuitable for some uses, customers will be informed. This emphasises the need for sound project planning at the onset, to understand thoroughly the project and head off issues before they arise. In turn, this means it is best to approach prior to starting a project so that planning is done in advance, rather collect data and then ask a bioinformatician to assist - delays at that stage may be costly.

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How are projects or software tested?

Dr. Jacobs has long been an advocate for sound testing of projects and software, having been concerned that this is a weakness in many academic projects. Testing is important for data quality too - for example, checking the consistency of data and the output.

The approach taken in-house is to test the products as they are developed. Each new addition to the product has corresponding test(s) added to the test code. After the addition of each new feature the complete testing code—for all elements of the project—is re-run. These tests can be packaged as part of the installation process of any software developed. (Ensuring that the local version is working as intended.)

Datasets are tested in a similar manner.

This high level of testing and verification is one of the prime differences between academic software development projects and quality commercial software development.

Where practicable and desirable, BioinfoTools may endeavour to formally prove the correctness of core algorithms, both using theorhetical techniques (eg. logical algebra) and practical tools (eg. our in-house and distributed regression tests).

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Will BioinfoTools guarantee the performance its software?

While care will be taken and ample testing applied (see previous FAQ), software development is too complex to apply a rigid guarantee. (Core algorithms or tightly focused tools can be tested more rigorously, as previously mentioned.)

The accuracy and reliability of software depends on much more than the code written by programmers. Correctness also depends on the software development tools used, on the computer hardware and on computer operating system the products are run on. These products are developed by other vendors and BioinfoTools cannot be responsible for errors in their products.

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Licensing

Licensing will vary depending on the nature of the project and can be tailored to customer’s needs. These needs can differ substantially between commercial and academic projects. Many computational biology needs can be met by open source software, which have no licensing issues.

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