About | People | Services | Projects | Training | Publications

Training Courses

As part of its work with the Babraham Insititue the Bioinformatics group runs a regular series of training courses on many aspects of bioinformatics.

Whilst these courses were designed for internal use many of them would be suitable for outside participants. If you are interested in having us run these courses for you then we may be able to arrange this through our consultancy service.

Where possible we also aim to make the material from our courses publicly available so that anyone who wants to can download them for their own use.

Below is a list of the courses we currently run. Where they are available there is a link to the training manual and course exercises.

Analysing Mapped Sequence Data with SeqMonk (Half a day)

SeqMonk is a program which can analyse large data sets of mapped genomic positions. It is most commonly used to work with data coming from high-throughput sequencing pipelines.

The program allows you to view your reads against an annotated genome and to quantitate and filter your data to let you identify regions of interest. It is a friendly way to explore and analysis very large datasets.

This course provides an introduction to the main features of SeqMonk and will run through the anlaysis of a couple of different datasets to show what sort of analysis options it provides.

For a more in-depth look at how to apply SeqMonk's tools to your data you can also look at our Advanced SeqMonk course

Course content

Course Material:

Advanced analysis with SeqMonk (Half a day)

The advanced SeqMonk course picks up where the basic course finishes. Rather than teaching you how to operate the program this course focusses on how best to apply the tools provided to your data.

The course focusses on optimising your data quantitation and filtering. It discusses biases which are often seen in data and the options SeqMonk provides to normalise these away. It also goes through the various statistical tools available in SeqMonk and under what circumstances each of these should be used.

For more complex experimental designs the course also introduces the clustering tools to try to generate functionally related sets of probes, which might make your data easier to interpret.

Course content

Course Material:

Sequence Analysis with VectorNTI (Half a day)

VectorNTI is a sequence analysis package which is useful for most day to day molecular biology tasks. Although it is not open source there is currently an offer from Invitrogen to supply a 1 year free licence to academics in return for signing up for their feedback system.

VectorNTI provides a friendly interface to all basic analyses (restriction maps, BLAST searching, primer design etc). This course provides an introduction to all of the core functionality of the VectorNTI package.

Course Content:

Course Material:

Sequence Assembly using the Staden Package (Half a day)

The Staden package is used for analysing sequencing data. It takes the traces you get from a sequencing service and allows you to compare them to a reference sequence or assemble them to create new sequences.

This course is invaluable to anyone who does any sequencing, from verifying the sequence of a 200bp insert, to sequencing a 500kb BAC!

Course Content:

Course Material:

Statistical Analysis using SPSS (Half a day)

Statistics are an important part of most modern studies and being able to effectively use a statistics package can help you to understand your results. This course provides an introduction to statistics illustrated though the use of the friendly SPSS package.

Course Content:

Course Material:

Statistical Analysis using GraphPad Prism (One day)

GraphPad Prism is a powerful and friendly package which allows you to plot and analyse your data. This course acts not only as an introduction to Prism, but also goes through the basic statistical knowledge which should allow you to make the most of your data.

Course Content:

Course Material:

Learning to Program with Perl (7 x 1.5 hour sessions)

For a long time Perl has been a popular language among those programming for the first time. Although it is a powerful language many of its features mean make it especially suited to first time programmers as it reduces the complexity found in many other languages. Perl is also one of the world's most popular languages which means there are a huge number of resources available to anyone setting out to learn it.

This course aims to introduce the basic features of the Perl language. At the end you should have everything you need to write moderately complicated programs, and enough pointers to other resources to get you started on bigger projects. The course tries to provide a grounding in the basic theory you'll need to write programs in any language as well as an appreciation for the right way to do things in Perl.

Course Content:

Course Material:

Exploring the Ensembl Genome Databases (2 hours)

The Ensembl web sites are one of the main points of access to the various completed eukaryotic genome sequences. They provide various tools to allow you to extract the information you need from the vast amounts of gene mapping information available. All the organism sites are also linked which allows you to easily find homologs to your gene in other organisms.

This course is useful to anyone who works in an organism whose genome has been sequenced.

Course Content:

Using the Bioinformatics Tools at NCBI (Half a day)

The NCBI is the main centre for bioinformatics in the USA. It provides a series of publicly available tools and databases which can provide a great deal of useful information about your gene or protein of interest.

This course will show you how to make effective use of the tools the NCBI offer.

Course Content:

Running and Analysing Microarray Experiments (Half a day)

Microarrays can potentially provide an insight into the state of transcription of many thousands of genes in a single experiment. This course provides an introduction to the theory and practice of microarrays and will cover everything from selecting an array and experimental design to data analysis and publication.

This course would be of benefit to those considering a microarray study, or even researchers who are in the early stages of running such a study.

Course Content:

Effective Database Searching (2 hours)

Most scientists are happy enough to run simple searches such as blast, but getting the best results from such searches requires the use of the correct search strategy. A good search strategy can find a lot of information which is useful, and a bad strategy can often lead you to incorrect conclusions.

This course provides an overview of the databases and search tools available, and details the optimal usage of both to help you find what you're looking for.

Course Content:

Viewing 3D Structures with Deep View (Half a day)

Many proteins have had their structures experimentally determined, and an examination of these structures can provide valuable insights into the function of these molecules. This course will show you how to use the free Deep View software to view and analyse both single and multiple protein structures. It will also show you how to make impressive molecular graphics for your reports or posters.

Course Content:

Course Material:

Making use of Comparative Genomics (2 hours)

Useful information can be gained by looking at the patterns of conservation between syntenic regions in two or more species. Whether you're interested in finding regulatory regions or are just comparing genomic organisation this course will show you how to make use of comparative genomics.

Course Content:

Introduction to R (Half a day)

R is a popular language and environment that allows powerful and fast manipulation of data, offering many statistical and graphical options. This course aims to introduce R as a tool for statistics and graphics, with the main aim being to become comfortable with the R environment. It will focus on entering and manipulating data in R and producing simple graphs. A few functions for basic statistics will be briefly introduced, but statistical functions will not be covered in detail.

Course Content:

Course Material: