# Conda for software installation: a livestream ## Advertisement On Feb 3rd, 2021 from 2:10pm PST, Titus Brown will be doing a livestream showing how to use conda to install bioinformatics software on the farm HPC. The stream will be on twitch, at https://www.twitch.tv/ctitusbrown, and he will be taking questions there. The stream will be recorded and the recording will be linked to this document. Attendance is free and you only need a (free) twitch account if you want to ask questions. The recording is [now available, here!](https://video.ucdavis.edu/media/Conda%20for%20software%20installation%20-%20a%20livestream/1_8ftdbogn) ### What is conda? Per https://docs.conda.io/en/latest/, conda: >provides package, dependency and environment management for any language—Python, R, Ruby, Lua, Scala, Java, JavaScript, C/ C++, FORTRAN, and more. >Conda is an open source package management system and environment management system that runs on Windows, macOS and Linux. Conda quickly installs, runs and updates packages and their dependencies. Conda easily creates, saves, loads and switches between environments on your local computer. It was created for Python programs, but it can package and distribute software for any language. ### What will be covered in this livestream? In this livestream, we plan to cover - * installing conda in a Linux account without admin privileges * showing how to use conda to install software and manage software environments * installing [mamba](https://wolfv.medium.com/mamba-development-news-29e32aaa8d6c) on top of conda * using multiple different versions of Python in the same account * using conda and pip to install Python packages in isolated Python environments * running [the variant calling workflow from a previous livestream](https://hackmd.io/SU2NB89JRu6fRPtSFizEEA?view) * installing R and R packages with conda, too! ### Are there any lesson materials? See [class notes from Tools for Data Intensive Research, Titus Brown and Shannon Joslin (2021)](https://github.com/ngs-docs/2021-GGG298/blob/latest/Week3-conda_for_software_installation/README.md). We'll also make use of materials from [a previous livestream on snakemake](https://hackmd.io/SU2NB89JRu6fRPtSFizEEA?view), and some [R / bioconductor install information from an RNAseq binder](https://github.com/ngs-docs/2020-ggg-201b-rnaseq/blob/latest/binder/environment.yml). Finally, for the up-front installation stuff on farm, see [our lab notes for farm, here](https://github.com/dib-lab/farm-notes/blob/master/getting-started.md#installing-conda). ### Bio Titus Brown is a professor at UC Davis who also serves as [DataLab’s](https://datalab.ucdavis.edu/) Director of Community Initiatives. The Brown lab focuses on genomic, transcriptomic, and metagenomic sequence analysis. The lab is the primary developer of the [sourmash software](https://github.com/dib-lab/sourmash/), for faster and more efficient sequence analysis of high-throughput sequencing data. They also run quite a bit of training in data-intensive biology. Professor Brown serves on DataLab recruitment committees, teaches workshops, leads hackathons, and participates in DataLab's strategic activities and planning.
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Links for OSS education/open source curricula

Organizations OSPO++https://ospoplusplus.org/ TODO Group (through the Linux Foundation) Industry focused, with some universities. High cost for sign up. OSPO Alliance European, not university focused but has some efforts

3/7/2023
Fractional sketches

or, some details of how sourmash and FracMinHash work! Consider overlaps between k-mers extracted from three genomes - two that share sequence, and one that does not. From these we can calculate k-mer based similarity measures (Jaccard similarity and containment). FracMinHash sketching compresses k-mer collections while retaining set relationships This is implemented in the software sourmash.

9/1/2022
Internal postdoc opportunities in biomedical data science training at UC Davis

We seek current postdocs (or graduating PhD students) at UC Davis to join a small team of staff and researchers to do training and engagement as part of the NIH Common Fund Data Ecosystem (CFDE). This opportunity may be of particular interest to postdocs who are seeking industry positions in biotech and would like hands-on experience and training in online training, asynchronous projects, GitHub-based material development, workflow execution, and cloud computing. Unfortunately this opportunity is limited to those who are already employed at UC Davis but whose funding is expiring. Applicants must be eligible for an extension to their postdoc position; we can also potentially hire newly graduated PhDs and PhD students on filing fee. Please contact us if you are interested. Details The NIH CFDE Training and Engagement Team runs a number of hands-on training workshops; you can see our current set of materials here and here. We are interested in recruiting postdocs to help in delivering, evaluating, maintaining, and extending these lessons. In return, we will train you in a variety of computational techniques and project management approaches! The supervisor/PI is C. Titus Brown.

10/26/2021
NSF LoS

[Letterhead] Dear NSF Proposal Review Committee: If the proposal submitted by Dr. Daniel S. Katz entitled “HDR Institute: Harnessing the Data Revolution through High Throughput Science and Engineering Expertise” is selected for funding by NSF, it is my intent to collaborate and/or commit resources as detailed in the Project Description or the Facilities, Equipment and Other Resources section of the proposal. Sincerely, [Your name]

1/15/2021
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