Python training ($480 for 8 two hour sessions)
This course teaches the basics of navigating the Unix commandline, logging into remote machines, and programming in Python. The course is organized around bioinformatics topics and is divided into 8 class sessions that are 2 hours each. By the end of the course users should be able to read a wide number of types of data files including tabular data, sequencing data, and VCF files, capture important statistics, and send outputs to tables and figures. Users will learn to write their own functions, and will see an overview of existing Python modules. Classes are capped at 10 students. For global health researchers in resource-constrained settings, these fees are largely waived (see our Global Health Bioinformatics Training Initiative).
Snakemake training ($240 for 4 two hour sessions)
This course is for people who have some experience in programming but would like to learn how to string together multiple scripts into a single parallelized workflow using the Snakemake workflow manager. Advantages of this system include:
- Better code readability with clearly labeled input and output files
- Easy management of parallelized processes
- Automatic re-running of only failed processes in the event of a job failure
- Easy scaling of resource use from single machines to large clusters
The course consists of 4 sessions of 2 hours each, and includes example pipelines, problem sets, and complex workflows including slurm cluster management and workflows that produce no output files or arbitrary numbers of output files. Classes are capped at 10 students. For global health researchers in resource-constrained settings, these fees are largely waived (see our Global Health Bioinformatics Training Initiative).
Pipeline development and general consulting (price negotiable on a per-project basis)
Examples of this could include:
- automation of a multi-step process into a polished workflow
- Visualization of a dataset (e.g. in plotly, matplotlib, or R)
- Development of a customized algorithm to search for custom motifs
- manipulation of tabular data
- Containerizing a workflow into Docker or singularity
- Analyzing genomic or RNA sequencing data to quantify abundance of a sequence of interest
Boxwood Bioinformatics 