University of Wisconsin - Madison: Biostatistics & Medical Informatics 776
Computer Sciences 776
Advanced Bioinformatics (Spring 2024)

General Course Information Course Overview Announcements Syllabus, Readings, Lecture Notes Schedule Homework and Project Past Semesters

Homework and Project Homework Assignments HW0 - Due Wednesday February 7, 2024 by 11:59 PM CT HW1 - Due Monday February 26, 2024 by 11:59 PM CT HW2 - Due Monday March 18, 2024 by 11:59 PM CT HW3 - Due Wednesday April 17, 2024 by 11:59 PM HW4 - Due Wednesday May 1, 2024 by 11:59 PM Homework Policies Submission Please note that Homework is due at 11:59 PM Central U.S. Time on the due date. Homework must be submitted using the handin directory on the biostat server (as specified in the HW assignment) and CANNOT be emailed to Instructor or TA. Solutions to written problems must be typed. Please show as much work as possible to receive partial credit. Late Homework Each student is allowed five free late days to be used on homeworks throughout the semester. These late days are provided in order to provide flexibility in case of illness, travel, paper deadlines, etc. so plan accordingly. There is no limit on the number late days that may be used on any particular assignment. Only business days are considered (e.g., homework due on Thursday and turned in the following Monday is 2 days late). After all late days are exhausted, the maximum possible homework grade will be reduced by 10% per day. Homework will NOT be accepted more than one week past the due date. Programming Policies Programming assignments must be completed using Python. Students are responsible for ensuring that their code runs in the Python environment on the Linux biostat server. This environment contains Python 3.6 and the following packages: matplotlib networkx numpy pandas pytest scipy seaborn weblogo Additional Python packages may be requested on the Piazza forum. This file can be used to create a conda environment that matches the Python on the biostat server. Project Information The project will be team-based, and every team should include 2-3 students. Project Suggestions and Guidelines Project ideas Project proposal guidelines Project progress report guidelines Project presentation guidelines Project final report guidelines Project Milestones Project proposal - Due March 4, 2024 by 11:59 PM Project progress report - Due April 8, 2024 by 11:59 PM Project presentation days - Class Time April 29 and May 1, 2024 Project final report - Due May 11, 2024 by 11:59 PM Project Resources Multimodal Single-Cell Data Integration Closed DREAM challenges Data sets for motif discovery (see paper by Tompa et al. on Syllabus page) Code, data and documentation for Noto & Craven CRM finding approach Splice-junction data set Whole genomes, gene coordinates, etc. from the ASAP database Tutorial on Scanpy in Python for Single Cell Omics R Bioconductor Packages (suite of tools for various bioinformatics projects)