Planning your project

Before determining which option is best for you, it is helpful to spend some time planning your project. We recommend talking to colleagues, peers, and your lab. We also recommend meeting with us to us regarding project planning if this involves genomic or bioinformatics data. During those initial meetings, we can talk about your scientific research questions, how you will collect data from wet lab experiments or large public databases, knowing the different data types, pre-planning for the amount of data to be analyzed and how, data policies associated with different grants, and pre and post-project genomics data management.

Picking the right resources

Once we have discussed your analysis plan, we will talk through the available computing related tools on campus and how we can use them as part of your research workflows. We can present all available options, and also likely recommend specific routes to pursue. As we collaborate often and frequently with campus partners, we are aware of the best practices of using these services for your research project.

How computing options are organized at UW–Madison

At UW–Madison, there are “departmental” and “shared” computing infrastructures, and some options in between. 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 no fee to the user and available to any UW–Madison researcher.

There is often no need to get a new computer to access any of these resources, as you will connect to “their machines” using the Terminal application on your Mac, Windows, or Linux machine; but these resources are distributed across many departments, centers and offices on campus.

Overall research computing support is summarized at this link , but we have summarized the options as relevant to likely visitors of this website.

In Bacteriology

• Departmental Server **new**: The Department of Bacteriology has now (Fall 2026) a small compute server available. You can use your netID login to access it on and off campus, but you need to request an account ahead of time. Please see this guide for more information.
• 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 is based most of the time.
• Center for High-Throughput Computing (free, available to all, but 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 the CHTC research facilitator team to onboard, teach, and implement how to use CHTC systems to run bioinformatics workflows. However, this is not an option for you if the data you will be using is sensitive or restricted. 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 their website to Request an Account. We provide end-to-end mentoring on how to initiate a project, learn how to submit jobs, and work together to develop bioinformatics workflows to be run on CHTC. 
  • We manage several common, large bioinformatics databases on the CHTC HTC system, such that each user does not need to download their own copies, which saves space and reduces redundancy! Check out our databases page.
• “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, for example. The GLBRC has a compute server and staff dedicated to helping with bioinformatics, including weekly office hours on computing topics. We can assist researchers wanting to learn how to use HTCondor to run bioinformatics jobs on the GLBRC servers. We recommend contacting GLBRC staff for specific questions about their cluster use and policies.
• UW–Madison Cloud Campus Infrastructure: UW–Madison CCI team manages cloud servers through vendor deals (Amazon, Google, Microsoft) with UW–Madison, and they are available to any lab/department for a fee. With this option, your lab would pay an account 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. We have not yet provided CCI support within the department at the moment, but let us know if this is something you are interested in learning more about.
• BadgerCompute. The BadgerCompute service is a new computing option that is free to use for researchers at UW–Madison, and was initiated by the CHTC, Data Science Institute and DOIT. It is a Jupyter-based interactive compute service for academic and research computing at the University of Wisconsin–Madison.” Particularly interesting for bioinformatics is that you don’t need to set up Python, RStudio, conda environments on your laptop, but can run your analyses, visualize data, and create reports directly from a web browser.

Outside Bacteriology

We do not train researchers directly on how to use these services. Please refer to their own pages for more information. 

• Certain labs in the same building as the Department of Bacteriology, the Microbial Science Building, are part of the UW School of Medicine and Public Health. The UW SMPH has at least these two computing resources:
  • Platform X: Research computing environment that is scalable to researchers needs to receive and analyze data; HIPAA compliant; hosted in cloud by UW SMPH
  • Platform R: Research Linux-based high-performance computing environment, with GPUs, many CPUs, and temporary fast ceph storage, HIPAA compliant; hosted locally by UW SMPH
• Social Science Computing Cooperative (SSCC) (restricted, sensitive data): The Department of Bacteriology is not a member of the SSCC, so we do not have access to these servers and statistical consulting services. If you need their services, visit https://www.sscc.wisc.edu/about-the-ssc/join-the-sscc/ to learn about Individual Memberships in the Cooperative.
• Departmental servers: Various departments on campus have compute servers. For example, some researchers in the Department of Faculty are affiliated with: 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 your data throughout a project.

Each faculty 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.

The ResearchDrive account can be connected to compute resources, such as CHTC, for a streamlined workflow.

Research Object Storage (S3) is also an option.

We have support-staff levels account for ResearchDrive and can teach you how to use ResearchDrive, how to use it in jobs on CHTC, etc. However, for permissions and account administrative issues, we can connect you with the ResearchDrive team.

Moving Data

Bioinformatics data can be several gigabytes (GBs) and even terabytes (TBs) in size. For large datasets, we recommend 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 amounts 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.

We can teach you how to set up Globus to transfer files between endpoints.