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Bioinformatics with Linux and Python (BILP01)

11 May 2020 - 15 May 2020

£275.00 - £550.00

Course Overview:

A fundamental part of bioinformatics (in contrast to simply computational biology) is the idea of scaling and automation. We want to arrange our tools into pipelines which can be executed with minimal supervision. Reliable automation of this type is key to many of the things that we want from our analyses; chiefly the ability to reproduce our results, and to extend them to other datasets.

In this course we will examine two different systems for automating bioinformatic analyses. For situations where we are mostly running existing command line tools, bash scripting will allow us to build pipelines with minimal overhead. We’ll start with simple command lines and see how the Linux environment – though not designed with biology in mind – is well suited to the type of automation we need.

For situations where we don’t have an existing tool available, and hence need to implement our own logic, bash quickly becomes unwieldy – it’s theoretically possible to write complex programs in bash, but the experience is painful! It’s much better to use a more modern programming language, and for most biological tasks Python fits the bill.

Intended Audience

This course is aimed at complete beginners – no previous Linux or Python experience is required. It will be helpful if you have a basic knowledge of molecular biology so that you will be able to follow the examples – i.e. you should know what DNA and protein sequences look like, what an intron is, etc. The course is most likely to be useful if you have some idea of the type of analyses that you will need to automate. If you have any questions about whether this course is likely to be suitable/useful, drop an email to the course tutor martin@pythonforbiologists.com and we will figure it out.

Venue – PR informatics head office, 53 Morrison Street, Glasgow, G5 8LB – Google map
Availability – 15 places
Duration – 5 days
Contact hours – Approx. 35 hours
ECT’s – Equal to 3 ECT’s
Language – English

Packages

We offer COURSE ONLY and ACCOMMODATION PACKAGES;
• COURSE ONLY – Includes lunch and refreshments and welcome meal Monday evening.
• ACCOMMODATION PACKAGE (to be purchased in addition to the course only option) – Includes breakfast, lunch, refreshments and welcome dinner Monday evening. Self-catering facilities are available in the accommodation. Accommodation is multiple occupancy (max 3- 4 people) single sex en-suite rooms. Arrival Sunday 10th May (between 17:00-21:00) and departure Friday 15th May (accommodation must be vacated by 09:15).

To book ‘COURSE ONLY’ with the option to add the additional ‘ACCOMMODATION PACKAGE’ please scroll to the bottom of this page.

Other payment options are available please email oliverhooker@prinformatics.com

PLEASE READ – CANCELLATION POLICY: Cancellations are accepted up to 28 days before the course start date subject to a 25% cancellation fee. Cancellations later than this may be considered, contact oliverhooker@prinformatics.com. Failure to attend will result in the full cost of the course being charged. In the unfortunate event that a course is cancelled due to unforeseen circumstances a full refund of the course fees (and accommodation fees if booked through PR informatics) will be credited. However, PR informatics will not be held responsible/liable for any travel fees, accommodation costs or other expenses incurred to you as a result of the cancellation. Because of this PR informatics strongly recommends any travel and accommodation that is booked by you or your institute is refundable/flexible and to delay booking your travel and accommodation as close the course start date as economical viable.

1235

Dr. Martin Jones

 

Teaching Format
Course Programme

Details

Start:
11 May 2020
End:
15 May 2020
Cost:
£275.00 - £550.00

Venue

PR informatics head office
53 Morrison Street
Glasgow, Scotland G5 8LB United Kingdom
+ Google Map
Phone:
07966500340
Website:
www.prinformatics.com