Weekly Tasks
Week 11 Tasks
Tasks for this Week
In our final revision session on Tuesday, we will run through the exam structure, course content, some example short answer questions and review how you structure pseudo-code with suitable commenting using some practical examples.
Please do use this time to ask any questions you may have, but we will also be monitoring the Piazza forum right up until the exam so you can as usual ask questions there too.
Remember you can download last year’s exam here to give you a concrete example of the question style.
A key tip for the exam is to pay attention to how many marks a part is worth and apportion your time appropriately.
Remember that I’ve added some reading and reference material suggestions that some of you may like to refer to for some background biology information. This is entirely optional, you are not expected to read through all these, but may find them useful on occassion during the course. You can find these here.
Week 10 Tasks
On Tuesday, we will learn the value of integrating multiple data modalities using practical examples from biomedicine across a range of different diseases. Following on from recent week’s work our focus will be on modeling at the patient level using networks.
On Thursday we will be working through two notebooks that use networks to model multiple data modalities. They will take advanatge of the SNFPy package that implements the similarity network fusion method proposed in Wang et al. Similarity network fusion for aggregating data types on a genomic scale. Nature Methods, 11(3), 333. The first notebook implements a toy example and the second uses real world data to build multiple modality networks and a fusion approach to integrate data for downstream analysis.
We’ve now finished our coding practice assignments, but there will be some notebooks for you to look at through the week (and beyond!) for this week’s course content.
Next week we only have one session, on Tuesday morning where I will be running through the course material, discussing the exam, and offering a Q&A session.
If you have any problems please do ask by posting a question on the Piazza forum (you can privately message me on there if you do not want to ask a question in public). I will be monitoring the forum closely throughout the course and this is the best way to get in touch with me.
Remember that I’ve added some reading and reference material suggestions that some of you may like to refer to for some background biology information. This is entirely optional, you are not expected to read through all these, but may find them useful on occassion during the course. You can find these here.
Week 9 Tasks
On Tuesday, we will learn what terminolgies and ontologies are, their properties and uses to structure biomedical data. This will include several of the ontologies used in health data research and emerging standards to address data interoperability.
On Thursday we will be working through two notebook that operate on ontology structures. The first introduces the pronto library that can parse ontology files in various standard formats and provides utility functions to query and manipulate them. The second notebook implements a natural language processing pipeline using the Allen Institute Scispasy framework to identify biomedical concepts from free-text. We will use this to tag data from publications and map these onto ontologies.
keep practicing with your preferred python coding environment using the course notebooks.
have a go at the new week 9 practice assignment in the GitHub Classroom, this one is to practice augmenting data with ontology derived information and returns to the GenCC data we used earlier in the course. Once again I’ve decided to release my solution along with the rest of this week’s materials for this so you can look at this if you would like to.
If you have any problems please do ask by posting a question on the Piazza forum (you can privately message me on there if you do not want to ask a question in public). I will be monitoring the forum closely throughout the course and this is the best way to get in touch with me.
Remember that I’ve added some reading and reference material suggestions that some of you may like to refer to for some background biology information. This is entirely optional, you are not expected to read through all these, but may find them useful on occassion during the course. You can find these here.
Week 8 Tasks
keep practicing with your preferred python coding environment using the course notebooks.
have a go at the new week 8 practice assignment in the GitHub Classroom, this one is to practice some consenus clustering. Once again I’ve decided to release my solution along with the rest of this week’s materials for this so you can look at this if you would like to.
On Tuesday, we will learn about network analysis and in particular clustering and functional enrichment analysis with a real world network example derived from the study of Autism Spectrum Disorders.
On Thursday we will be working through a notebook that performs functional enrichment analysis on the TCGA expression dataset that we were working with last week using the GSEAPy package.
If you have any problems please do ask by posting a question on the Piazza forum (you can privately message me on there if you do not want to ask a question in puclic). I will be monitoring the forum closely throughout the course and this is the best way to get in touch with me.
Remember that I’ve added some reading and reference material suggestions that some of you may like to refer to for some background biology information. This is entirely optional, you are not expected to read through all these, but may find them useful on occassion during the course. You can find these here.
Week 7 Tasks
keep practicing with your preferred python coding environment using the course notebooks.
have a go at the new week 7 practice assignment in the GitHub Classroom, , this one is for you to practice building a simple netwrok in Python using the NetworkX package. Remember these are not assessed, they are for you to practice related coding as the course progresses.
the assignment solution and data file are now available in the week 7 folder of the course GitHub repository
On Tuesday, we will learn some network basics and take a tour of different kinds of biological network using some real world research examples.
On Thursday I will be working through two notebooks using a NetworkX to build and analyse data. The second notebook will be using some real world data from The Cancer Genome Atlas (TCGA) that was used by us as part of a workshop at an international conference in 2024.
If you have any problems please do ask by posting a question on the Piazza forum (you can privately message me on there if you do not want to ask a question in puclic). I will be monitoring the forum closely throughout the course and this is the best way to get in touch with me.
Remember that I’ve added some reading and reference material suggestions that some of you may like to refer to for some background biology information. This is entirely optional, you are not expected to read through all these, but may find them useful on occassion during the course. You can find these here.
Week 6 Tasks
keep practicing with your preferred python coding environment using the course notebooks.
have a go at the new week 6 practice assignment in the GitHub Classroom, this one is for you to query the NCBI GEO system to search for interesting gene expression datasets. Remember these are not assessed, they are for you to practice related coding as the course progresses.
On Tuesday, we will go through background material to cover the principles of how RNA-sequencing is used to measure gene expression and the main methods used to analyse that data to identify genes that are differentially expressed between conditions.
On Thursday I will be working through two notebooks using a Python implementation of the most popular differential gene expression tool DESeq2. The first is a basic script to run through the process and the second is a real example of a published experiment looking for genes that are associated with Autism Spectrum Disorders.
If you have any problems please do ask by posting a question on the Piazza forum (you can privately message me on there if you do not want to ask a question in puclic). I will be monitoring the forum closely throughout the course and this is the best way to get in touch with me.
Remember that I’ve added some reading and reference material suggestions that some of you may like to refer to for some background biology information. This is entirely optional, you are not expected to read through all these, but may find them useful on occassion during the course. You can find these here.
Week 4 Tasks
keep practicing with your preferred python coding environment using the notebooks accompanying each week’s work.
have a go at the new week 4 practice assignment in the GitHub Classroom. Remember these are not assessed, they are for you to practice related coding as the course progresses.
I have decided to include the solution for the week3 optional assignment from GitHub Classroom right away this week which we will go through on Thursday
If you have any problems please do ask by posting a question on the Piazza forum (you can privately message me on there if you do not want to ask a question in puclic). I will be monitoring the forum closely throughout the course and this is the best way to get in touch with me.
Remember that I’ve added some reading and reference material suggestions that some of you may like to refer to for some background biology information. This is entirely optional, you are not expected to read through all these, but may find them useful on occassion during the course. You can find these here.
Week 3 Tasks
Keep practicing with your preferred python coding environment using the notebooks accompanying each week’s work.
Have a go at the new week 3 practice assignment in the GitHub Classroom. Remember these are not assessed, they are for you to practice related coding as the course progresses.
I have included a solution for the week2 optional assignment from GitHub Classroom which we will go through on Thursday
If you have any problems please do ask by posting a question on the Piazza forum (you can privately message me on there if you do not want to ask a question in puclic). I will be monitoring the forum closely throughout the course and this is the best way to get in touch with me.
Remember that I’ve added some reading and reference material suggestions that some of you may like to refer to for some background biology information. This is entirely optional, you are not expected to read through all these, but may find them useful on occassion during the course. You can find these here.
Week 2 Tasks
If you haven’t completed the tasks from weeks 0 and 1 please do so this week.
keep practicing with your preferred python coding environment using the notebooks accompanying each week’s work.
have a go at the new week 2 practice assignment in the GitHub Classroom. Remember these are not assessed, they are for you to practice related coding as the course progresses.
If you have any problems please do ask by posting a question on the Piazza forum (you can privately message me on there if you do not want to ask a question in puclic). I will be monitoring the forum closely throughout the course and this is the best way to get in touch with me.
Remember that I’ve added some reading and reference material suggestions that some of you may like to refer to for some background biology information. This is entirely optional, you are not expected to read through all these, but may find them useful on occassion during the course. You can find these here.
Week 1 Tasks
If you haven’t completed the tasks from week 0 please do so this week.
familiarise yourselves with VSCode whether that’s as a standalone on your laptop/desktop or whether you access it through the Noteable service (you are of course allowed to setup whatever coding environment you like)
experiment with setting up either conda or venv virtual environments for python and installing pacakges
practice using GitHub; the week 0 assignment gives you a basic introduction but the familiarity will help you unlock a lot of it’s useful features.
If you have any problems please do ask by posting a question on the Piazza forum (you can privately message me on there if you do not want to ask a question in puclic). I will be monitoring the forum closely throughout the course and this is the best way to get in touch with me.
I’ve added some reading and reference material suggestions that some of you may like to refer to for some background biology information. This is entirely optional, you are not expected to read through all these, but may find them useful on occassion during the course. You can find these here.
Week 0 Tasks
Setup or familiarise yourself with a preferred coding environment for coding in Python.
Sign up for a GitHub Student account using your University e-mail address e.g.
s12345@ed.ac.uk. This is because access to the GitHub Classroom for this course has an e-mail address roster to limit access; your GitHub e-mail must match.Join the course GitHub Classroom by accepting the first mini-assignment - “Introduction to GitHub” and work through this short excersie. Please note this is not assessed, it is to familiarise yourself with GitHub.
Check that you can login to the course discussion board on Piazza and (only if you would like to), introduce yourself by posting and tagging it with the “introductions” folder and perhaps leave a note of what you are hoping to learn during the course. Note that you can login to Piazza directly here, but may find it easier to click through from the course LEARN page. You should be automatically added to the Piazza class list from EUCLID.
If you have any problems please do ask by posting a question on the Piazza forum (you can privately message me on there if you do not want to ask a question in puclic). I will be monitoring the forum closely throughout the course and this is the best way to get in touch with me.