Welcome to the Bioinformatics Practical Handbook for BABS3291 Genes, Genome and Evolution. The material in this handbook is designed to help guide you through the practical.

Groups Research Topic GSE Chromosome First name Last name
Group 1 Neuroblastoma GSE202634 chr1_chr3 Aleksandar Blagojevich
      chr4_chr7 Sukriti Joshi
      chr8_chr12 Sarah Assi
      chr13_chr16 Ella Van Wensveen
Group 2 Parkinson’s Disease GSE125239 chr1_chr3 Eva Scoufis
      chr4_chr7 Yingjian Wang
      chr8_chr12 Mali Woods
      chr13_chr16 Rola Wael Foud Zohairy Zohairy
      chr17_chr22 Ceyda Kula
Group 3 Liver Alcoholic GSE155907 chr1_chr3 Emma Redd
      chr4_chr7 Hanyuan Liu
      chr8_chr12 James Wang
      chr13_chr16 Rafael Colinares
      chr17_chr22 Anju Harada
Group 4 Neural differentiation GSE123753 chr1_chr3 Nandan Dhanekula
      chr4_chr7 Ziggi Zikmann
      chr8_chr12 Neysa Njo
      chr13_chr16 Ellen Breynard
Group 5 Alzheimers and aging GSE104704 chr1_chr3 Sara Laker
      chr4_chr7 Isabelle Duff
      chr8_chr12 Olivia Reeves
      chr13_chr16 Kai Kam Chiu
Group 6 COVID-19 GSE152418 chr1_chr3 Zihan Zeng
      chr4_chr7 Jasmin Yip
      chr8_chr12 Daniel Vergov
      chr13_chr16 Mark Burgess
Lupus Group 7 GSE72420 chr1_chr3 Sakun Munasinghe
      chr4_chr7 Iris Chang
      chr8_chr12 Andreas Bartnitzky
      chr13_chr16 James Hilton
Lymphoma Group 8 GSE159808 chr1_chr3 Patricia Chang
      chr4_chr7 Hugh Benz
      chr8_chr12 Thomas Altamura
      chr13_chr16 Marta Stojnic
      chr17_chr22 Jessica Gu
Myelodysplastic syndrome Group 9 GSE65349 chr1_chr3 Mengning Zhang
      chr4_chr7 Mariya Skripnikova
      chr8_chr12 Junhee Kim
      chr13_chr16 Jon Mann

Key to How Infomation will be Displayed

Exploratory text

$ Command-line examples will be given in their own boxes, starting with "$".
 $ Optional parameters will be given [in square brackets].
Terminal output will be in the same format, without the leading $.

Functions used within exploratory text

Questions/Challenges

You will find questions and extra activities scattered throughout the instructions. These are not assessed but will help you to understand the processes and associated theory lectures.

These contain general reusable hints and tips rather than specific topic commands etc.

NOTE: It is recommended that you also use a fixed width font (e.g. Consolas) and colour formatting when documenting code in your own lab books to help it stand out from other thoughts/instructions.