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What BioinfoTools offers

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

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Background
Dr. Grant Jacobs

What BioinfoTools offers

 

Below is an outline of what BioinfoTools offers. Further information is available on the FAQ page. If you have any questions, feel free to use the enquiry form.

Contents

Overview

Introduction

Small teams v. large

Computational biology (incl. data analysis)

Software development

Advisory consulting and training

Web-hosted database and computational services

Dr. Grant Jacobs (résumé)

Overview

Introduction

A précis of what BioinfoTools offers can be found on the home page of this website. In the sections below this is expanded upon.

Briefly, BioinfoTools aims to offer an experienced computational biologist to customers. Four broad areas are offered under the general umbrella of computational biology: research computational biology and data analysis, software development (including developing and testing original algorithms), advisory consulting and training (including training courses, advice, assessment, reviews & documentation), and web site and web application development for hosting scientific databases or analytical analysis software.

Each of these are expanded upon below.

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Small teams v. large

Many bioinformatics consultancies offer access to a team of junior staff with differing skills via a senior consultant who manages the projects. It is rare in these firms for senior bioformaticists to be doing the hands-on work.

BioinfoTools offers access to a senior computational biologist to directly work on your project.

It’s a very different approach, one that best suits research groups wanting a close, tight approach to their project or where the research team wants extensive interaction with the computational biologist.

More important than a large computer in the back room is that the consultant has the computational biology knowledge to drive the project, including a good understanding of the biological work to be addressed. One strength of BioinfoTools is Dr. Jacobs’ strong background in molecular biology, genetics, as well as computer science and computing.

Dr. Jacobs’ biological background goes beyond genomics to include protein sequence and structure work. This is reflected in his personal research interests in epigenetics, chromatin and genome structure (in both linear and three-dimensional senses), which blend the genomics, evolutionary and structural aspects of computational biology. It is also reflected in aiming to work directly from client’s biological aims, taking 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 algorithms for sequence and structure analysis. Of computing technology, there is experience in a wide range of programming languages and tools. Details of these are listed below and in the FAQ page.

World-wide there are facilities that offer very large computer resources at modest costs. An advantage of tapping into these resources is that a consultancy need not maintain large computing facilities that can substantially add to the business overheads, and hence the cost of hiring the consultant. Exploiting the availability of these services, clients will be billed what their actual usage requires.

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Computational biology (incl. data analysis)

BioinfoTools is happy to assist with a wide range of projects from genome sequence analysis through to protein structure analysis. Prospective customers are encouraged to discuss their interests (at no cost).

Dr. Jacobs’ follows research in epigenetics, chromatin and genome structure (in both linear and three-dimensional senses), studies of classes of genes or proteins, and software or algorithm development; additional value can be offered in projects in these areas.

One strength is incorporating both sequences and structural information. Many sequence projects entirely omit the ample structural information available, potentially to their loss. This is notable, for example, in sequence-based studies of epigenetics; there is considerable structural information about the molecules involved that for many projects are not being exploited.

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Software development

Dr. Jacobs’ background is jointly in computer science and biology. Computer science is more than programming, and includes the theoretical basis of algorithm design, data structures (for storing data), design of operating systems and so on.

Good computational biology 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.

There are (at least) two distinct elements to this. The first is a good understanding of the first-principles biology (physics, chemistry) used to develop the computational biology methods. At this level the algorithms developed can be applied very widely, for a wide range of biological problems, as the first-principles knowledge used relates to molecular systems in general.

As simple example, a protein multiple sequence alignment can be applied to wide range of protein families, or a genome assembly algorithm to a wide range of genomes.

The other is tailoring or applying of a method to a particular project, or developing of a method with a particular niche area or question in mind. Here specific knowledge about the biological particulars relevant to the project matters.

Returning to the simple examples given earlier, different protein families or genomes have different characteristics or features that affect how to analyse their data.

As a research scientist at heart, opportunities to learn new areas are welcome - don’t feel that because your project is outside of the short list below it can’t be considered.

Dr. Jacobs’ current biological interests include gene regulation, epigenetics, chromatin structure, genome 3-D structure and, more broadly, structural biology (e.g. the structure and function of DNA, RNA and proteins and their interactions). He also has a developing interest in neurobiology.

Current in-house interests include exploration of compact and fast storage of sequence and 3-D structure data, sequence assembly, multiple sequence alignment, 3-D structure analysis, and analysis chromatin and genome structure. The biological focus for these are analyses of genomes, in a full epigenetic, chromatin and genome 3-D structure context. (Feel free to enquire about projects outside of this scope.)

Algorithms involving three-dimensional structure draw on biological background and algorithms not usually found when working on sequence data only. Increasingly utilising both sequence and structural data will be important to understanding the functioning of the genome in vivo.

Software is developed for the range of Unix and Unix-related operating systems (eg. Linux, Mac OS X, commercial Unix-based systems) including client-server applications accessed from any client platform (Mac OS, Windows, Unix-based). This choice of primary target platforms reflects that large-scale scientific computing remains dominantly based on Unix-based platforms.

Rigorous testing and extensive documentation is important. The approach taken at BioinfoTools is to test and document the software as an integral part of the development of the code. Further information on the testing approach is available on the FAQ page.

If you have an interest in algorithm or software development, feel free to discuss them.

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Advisory consulting and training

Requests for training courses, advice, project assessment, reviews (literature, software tools, infrastructures, etc) are welcome. This work can include technical writing, for example documentation of products, (technical) editing of articles and the like.

In the case of training, for routine tasks it is sensible to teach your staff how to do the task rather than repetitively ask a specialist to handle it. You should discuss with a specialist learn if the task is suitable to be placed in the hands of a non-specialist first.

Regards advice and project assessment: consulting on data analysis should start at the time of planning the project for best results.

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Web-hosted database and computational services

Dr. Jacobs has extensive experience in developing “web apps” - data analysis services hosted by a web server, accessed through a web browser. These projects go considerably beyond creating web pages, requiring skills in a mixture of web (HTML, CSS, Javascript) and server technologies (Perl and database programming, web server installation). Allied with a strong background in both biology and bioinformatics, custom solutions can be built from ground-up.

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Dr. Grant Jacobs (résumé)

BioinfoTools is a consultancy founded to deliver Dr. Jacobs’ expertise and experience in computational biology. Below is a brief résumé outlining Dr. Jacobs’ key skills and research interests. A full cirriculum vitae is available on request.

Dr. G. H. Jacobs - Independent senior computational biologist

Skills

Current personal research interests (consulting offers have wider scope)

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