Bioinformatics Research Support
Department of Bacteriology
Banner image with icons of a person thinking, a cloud system, a terminal and a server.

Computing Resources

Before determining which option is best for you, it is helpful to spend some time planning your project. We recommend to talk to colleagues, peers, and your lab. We also recommend talking to us regarding project planning that involves genomic or bioinformatics data. This involves thinking about your research question, how it integrates with wet lab experiments, data types to answer your question, planned amount of data to be analyzed and how, data policies associated with different grants, and pre and post-project genomics data management. Please contact us if you need help getting started!

How computing options are organized at UW-Madison:

At UW-Madison, we have “departmental” and “shared” computing infrastructure. Departmental services are available to members of given departments, and are sometimes associated with membership or a cost. Shared Computing Infrastructure on campus refers to resources that are available for “free” to the user, and available to any UW-Madison researcher.

There is no need to get a new computer to access any of these resources, as you will connect to “their machines” using the Terminal. Therefore, understanding how to use the command-line is a helpful prerequisite. For suggestions on how to get learn the basics, please see the page Learn.

In Bacteriology

  • Lab hosted servers: Some labs in the department of Bacteriology manage their own laboratory server. Your PI would know the information on how to log in to those. Not all labs have this. Often Linux based most of the time.
  • Center for High-Throughput Computing (free, available to all, no sensitive data): Commonly referred as “CHTC”, this is a computing option available to all members of UW-Madison, free of charge for research-purposes. CHTC has both High Throughput and High-Performance computing options. The Bacteriology Bioinformatics Research Support Service works closely with its members to onboard, teach, and implement how to use CHTC systems to run bioinformatics workflows. However, this is not and option for you if the data you will be using is sensitive or restricted (e.g. HIPAA protected). If you are unsure, speak to us. This is the most popular option among Bacteriology labs due to the cost, flexibility and use cases. If you would like to get started using CHTC, please visit the CHTC website, and fill the form to create an account, list your PI as lab PI, and list my name for Mentor. I will then receive an email letting me know you requested an account, and I will work directly with you.
  • “Centers”: Centers overlap departments, and different faculty members can be part of different centers. Many Bacteriology Faculty are members of the Great Lakes Bioenergy Research Center. The GLBRC has a compute server and staff dedicated to help with bioinformatics.
  • UW-Madison Cloud Campus Infrastructure: UW-Madison DoIT Research Cyberinfrastructure manages cloud servers through vendor deals (Amazon, Google, Microsoft) with UW-Madison, and are available to any lab/department. With this option, your lab would pays for a server that you can manage, with support from DOIT. This is a pay-per-use option. They host office hours (see Calendar tab) each week if you are curious about this option.

Outside Bacteriology

  • Platform X (restricted, sensitive data): This is the service available to members of the School of Medicine and Public Health (SMPH). Since the Department of Bacteriology is part of the College of Agricultural and Life Sciences (CALS), we do not have access to this service. However, if you are visiting this webpage to understand your options at UW-Madison, and you are in a laboratory that is part of the School of Medicine and Public Health, you may contact them to learn more/access their resources.
  • Social Science And Computing Center (SSCC) (restricted): The Department of Bacteriology is part of the College of Agricultural and Life Sciences (CALS), so we do not have access to these servers & statistical consulting services. If you are part of one of these member departments (listed here https://www.sscc.wisc.edu/about-the-ssc/join-the-sscc/) you can contact them to learn more.
  • Departmental servers: The Department of Chemistry department has a High Performance Computing (HPC) cluster, and the Department of Biochemistry has a High Throughput Computing (HTC) computing cluster.

Data Storage Options

Please use this tool to help you decide where you should store you data throughout a project.

All labs in the Department of Bacteriology have access to a “ResearchDrive” account, which stores 25TB of data, with more space available for an annual fee. This is a good option to store bioinformatics/research related data as the file sizes can be quite large.

Moving Data

Omics & bioinformatics data can be several gigabytes (GBs) and even terabytes (TBs) in size. The best way to move this type of data is by using Globus. Moving large amounts of data over wifi can be not secure and can fail (if the internet goes down). Globus is a UW-Madison supported service that enables people to transfer large amount of data between locations (for example, a CHTC folder, a ResearchDrive, a personal computer, a remote server of your choice) in a secure & fast way. Tutorials will be published under “Tutorials” soon, but in the meantime, please contact us to learn how to use Globus in your workflows.