Intern 2025 BCBC Bioinformatics Course
About the Course
We are living in massive data times, and science is not an exception. New sequencing technologies are filling hard disks with terabytes of information, billion of sequences that need to be analyzed in a proper way. But not only sequence data is growing, gene expression and metabolite concentrations are analyzed by the hundreds or thousands, in a way that makes it difficult, if not impossible, to use familiar tools such as Excel. In this new world, bioinformatic skills are needed, not only by computational biologists, but by biologists and biochemists who find themselves analyzing many genes, proteins or metabolites at the same time.
With this perspective, we aim to further bioinformatic skills within the postdoc community at Boyce Thompson Institute through this course. We try to keep it as simple as we can, with just one idea: “Show useful tools to resolve common problems found during the *omics data analysis”. For example, if I have two lists of hundred of genes, how can I combine them and find the common ones, or how can I analyze GO terms for my over-expressed genes, or how can download a chromosome region using Jbrowse or… there are dozens of examples.
Before the Course: Setting Up the BCBC Course Virtual Machine
The BTI Bioinformatics Course uses Virtual Box to virtualize a Linux operating system (OS) inside any computer. The virtual machine (VM) is a Linux OS, Debian distribution for 64-bit computers. In order to get it running, you’ll need to download both the VirtualBox software, and the virtual machine itself.
For those with M-chip Mac laptops:
Do not follow the instructions below. Instead, we ask that you please still come to one of the designated office hours (listed below) to discuss alternate arrangements with us.
All others (including non-M-chip Macs):
Before the course begins, you need to follow these instructions for installing Virtual Box and the course virtual machine on your computer. Please note that, from the VirtualBox website, there are two things you will need: the VirtualBox package and the VirtualBox Extension Pack.
Steps:
1. Please download and install VirtualBox version 7.0.14 from the following webpage:
Click on the link above and then scroll down to where it says “VirtualBox 7.0.14 (released January 16 2024)”. Please download the VirtualBox version for your computer’s OS (Windows or Intel Mac), and also download the “Extension Pack”. Please see the attached image for guidance.
In addition to the items from the VirtualBox website, you will need the Virtual Machine file available here.
Note that some of these downloads may take some time. You’ll need to remain connected to the internet during the download process in order for each download to be completed properly.
So, in total, there are 3 downloads needed for setup:
1) The VirtualBox platform package (from the VirtualBox website)
2) The VirtualBox Extension Pack (also from the VirtualBox website)
3. Create a VM Folder in your system and copy/move the .ova file.
4. Open the VirtualBox program.
5. Select the option File > Import Appliance
6. Click “Open Appliance”. Select the .ova file and click “Continue”.
7. Enable “Generate new MAC addresses for all network adapters” and click “Import”.
8. If you have problems with VM installation, you can attend the bioinformatics hour on Tuesday or Thursday at 1 – 2 pm.
Troubleshooting
- I have enabled virtualization but VirtualBox still gives an error asking to “Enable vt-X” or similar.
Make sure you have disabled hyper-v. This can be done by following these instructions.
- I have downloaded both the VirtualBox software and the virtual machine file and enabled virtualization, but it still will not run.
- If you use a MAC and have problems with importing the latest VM , please check this link to do the troubleshooting. https://medium.com/@DMeechan/fixing-the-installation-failed-virtualbox-error-on-mac-high-sierra-7c421362b5b5
9. For M1-M3 chip Mac users: If you have a newer Mac computer, contact us directly for special arrangements, since the software may not work for you.
Make sure you have a 64-bit machine and have followed the above steps precisely, especially enabling . Come to our office or email us for further troubleshooting if you cannot find the problem.
6/11/25 (1pm) — UNIX Command-Line Intro, Part 1
Presenter: Adrian
Topics covered
- Terminal file system navigation
- Wildcards, shortcuts and special characters
- File permissions
- Compression UNIX commands
- Networking UNIX commands
Estimated Time
- Lecture and exercises: 2:00 h
Materials
6/20/25 (9:30am) — UNIX Command-Line Intro, Part 2
Presenter: Adrian
Topics covered
- Basic NGS file formats
- Text files manipulation commands
- Command-line pipelines
- Introduction to bash scripts
Estimated Time
- Lecture and exercises: 2:00 h
Materials
6/26/25 (9:30am) — Quality Control
Presenter: Adrian
Topics covered
- Different sequencing technologies
- Sequence file types and formats
- Genome Assembly
- Annotation
- Quality encoding
- Quality control tools
Estimated Time
- Lecture and examples: 2:00 h
Materials
7/3/25 (9:30am) — R #1
Presenter: Adrian
Estimated Time
- Lecture and examples: 2:00 h
Materials
7/10/25 (9:30am) — R #2
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