Bioinformatics Team

MRC Clinical Sciences Centre

Tom Carroll

The Bioinformatics Team.

  • Tom Carroll
  • Gopuraja Dharmalingam
  • Sanjay khadayate
  • TBD

Websites

http://mrccsc.github.io

Computing and Bioinformatics

Where to find the team.

  • ICTEM
  • 2nd floor, MRC.
  • Central aisle,
  • Behind the printers.

Role

  • Analysis
  • Experimental design.
  • Bioinformatics Infrastructure.
  • Training.
  • Bioinformatics Seminar Series.

Text

Experimental Design

“To consult the statistician after an experiment is finished is often merely to ask him to conduct a post mortem examination. He can perhaps say what the experiment died of.”

Fisher RA, 1938

  • Work closely with Genomics Team to help with design questions
    • Replicate number.
    • Sequencing depth.
    • Sequencing strategy.

Nice example experimental design

  • RNA-seq experiment (2014)
  • Graph shows major sources of variation.
  • Samples from same groups close together.
  • Samples from different experimental conditions separate. 

Nice example of experimental design

  • Smaller sources of variance relating to other metadata.
  • Samples group according to the day that RNA was extracted on.
  • Known effects can be removed from analysis.

Analysis

  • Quality control for data.
  • Advice and support as needed.
  • Support throughout project.

Analysis support

  • Increased use of high throughput techniques in projects.
  • Greater use for bioinformatics in projects.
  • Analysis across project lifetime or individual elements.
  • Requires reproducible research.

Reproducible research

  • Reproducible results from computational methods should be straight forward.
  • Common problems.
    • Version and software changes.
    • Lack of analysis documentation

rMarkdown

  • rMarkdown converted R code to dynamic reports.
  • Code, results and versions are reported within the same page.
  • HTML allows for inclusion of dynamic elements.

Project tracking

  • Use Redmine software.
  • Multiple user interface to record project information.
  • Repository to version control scripts (SVN).
  • Wiki for internal documentation.

Infrastructure

  • Analysis pipelines.
  • Data delivery.
  • Software development.

ChIP-seq and RNA-seq

pipelines.

  • Common analysis steps can be automated.
  • Optimised for local resources.
  • Reproducible and comparable.
  • ChIP-seq and RNA-seq pipeline to automate alignment and quality control.​
  • Freely available for use or customisation on github

http://mrccsc.github.io/

UCSC genome browser

  • UCSC allows for visualisation of a range of genomics data types.
  • Public instances can be very slow.
  • CSC public instance maintained by Bioinformatics team.

  • web: http://ucsc

    FTP: ftp://ucsc

Software

  • Develop and maintain software relevant to our work.
  • R packages and javascript toolsets.
  • Release software to public (peer-reviewed) repositories.
    • Collaborative feedback.
    • Automated build reports and checking.

ChIPQC

  • Lack of suitable R/Bioconductor quality control tools for ChIP-seq.
  • Require methods to assess quality across high volumes of samples
  • ChIPQC developed and tested on 500 public datasets.

Package

Bioc2014 Tutorial

  • IGV is an popular alternate to UCSC.
  • Allows for inclusion of per sample metadata and complex sample display types.
  • Tracktables creates standalone and rMarkdown compliant tables.

Tracktables

Training

  • Computation Biology Week.
  • Aim to develop courses to meet requirements.
    • ​R
    • Python
    • Bioinformatics tools

CSC Bioinformatics Course

  • Current and upcoming Bioinformatics training material can be found at our site

http://mrccsc.github.io/training

 

Training Collaborations

Develop and share courses between other Bioinformatics teams.

https://github.com/bioinformatics-core-shared-training

Bioinformatics Seminar Series

 

  • Through-out year,  Fridays.

  • Features external and internal speakers.

  • Discuss methodology behind bioinformatics analyses.

  • Meet people working on similar bioinformatics problems.

Bioinformatics Seminar Series

Laurent Gatto

 

Johnathan Cairns

 

Shamith Samarajiwa

 

Ines de Santiago

 

5th, December

 

13th, February

 

20th, March

 

24th, April

 

Head of Computational Proteomics Unit, Cambridge

Postdoc, Peter Frasier lab,  Babraham Institute

Prinicipal Investigator, MRC Cancer Unit

Postdoc, Markowetz  lab, CRUK.

Contacts and thanks

Bioinformatics Team

Tom - thomas.carroll@imperial.ac.uk

Gopu - gopuraja.dharmalingam@imperial.ac.uk

Sanjay -  sanjay.khadayate@imperial.ac.uk

Thanks to..

Lenhard lab - Organisation of CWB

Computing Service - Infrastructure support