---
title: "Welcome to Big Data Biology (BIO00047I)"
output: html_document
---
**Quick links:**
[Module synopsis](https://www.york.ac.uk/students/studying/manage/programmes/module-catalogue/module/BIO00047I/latest) |  [VLE Site](https://vle.york.ac.uk/webapps/blackboard/execute/announcement?method=search&context=course&course_id=_88160_1) | [List of staff](https://vle.york.ac.uk/webapps/blackboard/execute/staffinfo/manageStaffInfo?course_id=_88160_1&mode=view&mode=view) | [Description of the data](http://www-users.york.ac.uk/~dj757/BIO00047I/misc/BIO00047I-data-description-2020.pdf) | [Report Guide ](http://www-users.york.ac.uk/~dj757/BIO00047I/misc/BIO00047I-report-guide-and-marking-scheme-2020.pdf)

***

##Lectures 

These lectures are provided with **no audio** at the moment. There are only **two lectures** for this module.

* Lecture 1 [PDF](http://www-users.york.ac.uk/~dj757/BIO00047I/lectures/BIO00047I-2020-Lecture1.pdf) | [Powerpoint](http://www-users.york.ac.uk/~dj757/BIO00047I/lectures/BIO00047I-2020-Lecture1.pptx) 

* Lecture 2 [PDF](http://www-users.york.ac.uk/~dj757/BIO00047I/lectures/BIO00047I-2020-Lecture2.pdf) | [Powerpoint](http://www-users.york.ac.uk/~dj757/BIO00047I/lectures/BIO00047I-2020-Lecture2.pptx) 





***

##The assessement
The assessment for this module is a report describing an analysis of data (maximum 1500 words).
A description of what we want to see, and how we will mark the report is [here](http://www-users.york.ac.uk/~dj757/BIO00047I/misc/BIO00047I-report-guide-and-marking-scheme-2020.pdf)

**The assessment deadline for last year was: Thursday 16th of April 2020 at 11am**

***

##The Google Hangout
We'll provide a link to join the Big Data Biology 2020 Google Hangout later.

This module will use a Google Hangout chatroom to share questions, plots, R code (and sometimes to announce any errors in the website that we find). Some people find the R code useful as a resource. **Use of the Hangout is optional.**

**PS:** As your posts are personal data, we comply with General Data Protection Regulation (GDPR). You can read about this, and some rules for good conduct [here](http://www-users.york.ac.uk/~dj757/BIO00047I/misc/BIO00047I-GoogleHangout.pdf).


***
##The Seven Principles of Big Data Biology

*Big data sets are an important part of modern biology. But they can be complicated. To help you though this path, we have distilled (some of) our wisdom into some principles that are important to learn. Here they are:* 

1. What is the biological question?
2. Know your data.
3. Filter out the bad stuff.
4. Statistical tests are powerful.
5. Be careful with statistics.
6. If you conduct multiple tests, you need multiple test corrections.
7. Present data honestly and clearly.


Download the details here: [The Seven Principles of Big Data Biology](http://www-users.york.ac.uk/~dj757/BIO00047I/misc/BIO00047I-seven-principles.pdf)


***

image: ![](pics/Pancaldi.jpg)

A protein interaction network from [this article](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3337474/)

***


#Workshop material

![](pics/Banner.png)


***

##Workshop 1
[Part A: Brassica data](http://www-users.york.ac.uk/~ah1309/BigData/Big_Data.html)

[Part B: Fission yeast data](http://www-users.york.ac.uk/~dj757/BIO00047I/workshop1B.html)

[Part C: Fungal metagenomic data](http://www-users.york.ac.uk/~de656/BigDataBiology/ecologyHedges_day1_open.html)


***

##Workshop 2
[Part A: Brassica data](http://www-users.york.ac.uk/~ah1309/BigData/Big_Data2.html)

[Part B: Fission yeast](http://www-users.york.ac.uk/~dj757/BIO00047I/workshop2B.html)

[Part C: Fungal metagenomic data](http://www-users.york.ac.uk/~de656/BigDataBiology/ecologyHedges_day2_open.html)

***


##Workshop 3
[Part A: Brassica data](http://www-users.york.ac.uk/~ah1309/BigData/Big_Data3.html)

[Part B: Fission yeast data](http://www-users.york.ac.uk/~dj757/BIO00047I/workshop3B.html)

[Part C: Fungal metagenomic data](http://www-users.york.ac.uk/~de656/BigDataBiology/ecologyHedges_day3_open.html)



**You should decide which data set you will use for your project after workshop 3.
Then start to work on data analysis in your own time. See more details about the assessment on the [VLE](https://vle.york.ac.uk/webapps/blackboard/execute/announcement?method=search&context=course&course_id=_88160_1).**

**The assessment in 2020 was due no later than: Thursday 16th of April at 11am**

**The data** is described [here](http://www-users.york.ac.uk/~dj757/BIO00047I/misc/BIO00047I-data-description-2020.pdf).


***


##Workshop 4
[Part A: Brassica data](http://www-users.york.ac.uk/~ah1309/BigData/Big_Data4.html)

[Part B: Fission yeast data](http://www-users.york.ac.uk/~dj757/BIO00047I/workshop4B.html)

[Part C: Fungal metagenomic data](http://www-users.york.ac.uk/~de656/BigDataBiology/ecologyHedges_day4_open.html)


***

##Workshop 5 

Workshop 5 is a report writing tutorial. See [here](http://www-users.york.ac.uk/~dj757/BIO00047I/workshop5.html)

***

**The assessment is due after Easter**, on 16th April 2020 (no later than at 11am).

***


##Workshop 6

[Introduction to Python](http://www-users.york.ac.uk/~dj757/BIO00047I/workshop6.html)


***


**Credits**.

* The Brassica workshops were written by **Andrea Harper**, using data from her own ressearch.

* The fission yeast workshops were written by **Daniel Jeffares**, using data from Angeli/his own ressearch.
 
* Fungal metagenomic workshops were written by **Daphne Ezer**, using data from Thorunn Helgasson.

* The Python workshop was written by **Pete Ashton** from the Bioinformatics and Genomics lab. 

* **Big thanks to Emma Rand** for showing us how to use R Markdown to make this site. **Thanks Emma!**
You can see Emma's R workshops from 1st year: [BIO00017C](http://www-users.york.ac.uk/~er13/17C%20-%202018/BIO00017C.html) . These will be useful for reminding yourself what you know about R. There are also some suggestions on the VLE.



