hackmd-github-sync-badge Activities notes Nobska Lighthouse run tomorrow morning, 7:30am; meet at Swope. 3.5 mi, ~40 minutes. axe throwing poll on slack! Saturday 7:30-9:30pm in Falmouth. Accessing notebooks for James Briscoe's lectures Go to https://gern2024-a.idyll.org/ in your Web browser and log in with your username and password. Then, use the Terminal application to run:

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

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.

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.

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! 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.

[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]

[toc] the group: Andy, Renata, Christine, Titus 1. Grow a community worth sustaining https://github.com/commonsing/2021-paper-simplish-rules/issues/1 2. Reward participation with opportunities for governance https://github.com/commonsing/2021-paper-simplish-rules/issues/2

UC Davis URL: http://bit.ly/ggg298syllabus [toc] Code of Conduct Please abide by my lab's Code of Conduct in this course. In particular, this is not an intellectual contest, and please realize that we all have plenty of things to learn.

posted at http://ivory.idyll.org/blog/ The feature that I'm most excited about in sourmash 3.3.0 is the ability to directly use compressed SBT search databases. Previously, if you wanted to search (say) 100,000 genomes from GenBank, you'd have to download a several GB .tar.gz file, and then uncompress it out to ~20 GB before searching it. The time and disk space requirements for this were major barriers for teaching and use. In v3.3.0, Luiz Irber fixed this by, first, releasing the niffler Rust library with Pierre Marijon, to read and write compressed files; second, replacing our old khmer Bloom filter nodegraph with a Rust implementation (sourmash PR #799); and, third, adding direct zip file storage (sourmash #648). So, as of the latest release, you can do the following:

UC Davis URL: http://bit.ly/ggg201syllabus GitHub archive: github.com/ngs-docs/2020-GGG201b-lab [toc] Code of Conduct Please abide by my lab's Code of Conduct in this course. In particular, this is not an intellectual contest, and please realize that we all have plenty of things to learn.

Feb 21, 2020 Variant calling workflow Assembly workflow what does each workflow do? how do we know they worked? computer saying "no errors happened!" is usually necessary but not sufficient

[toc] Wednesday lab - 2/19 Slurm and farm Friday discussion - 2/21 Homework Please read the executive summary for the July 2019 CFDE report, as well as one of the DCC site visit appendices of the three CFDE reports (July, October, December). Each of the DCC site visit appendices describe nine different Common Fund projects and their Data Coordinating Center operations; the projects are in the following appendices: Human Microbiome Project - July

Getting set up for the assembly workflow (Ask people to do this soon.) Log into farm; then clone the assembly repository, cd ~/ git clone https://github.com/ngs-docs/2020-ggg-201b-assembly.git assembly-repo/ change into that directory,

--- tags: ggg, ggg2020, ggg298 --- # GGG 298, Jan 2020 - Week 6 - git and GitHub for change tracking! [toc] git is a **version control system** that lets you track changes to text files. It can also be used for collaborating with others. It's like Word change tracking, on steroids. Git takes a while to learn, like anything else. This lesson will teach you most of what you need to do to collaborate with yourself. Collaborating with others is a lot harder and will maybe be the subject of a dif

--- tags: ggg, ggg2020, ggg201b --- # GGG 201b, jan 2020 - lab 3 - NOTES [toc] ## Friday Lab Outline - 1/24 You can do collaborative note taking [here](https://hackmd.io/cZ9ehhV7TQONFu5EYx2JgA) if you like! Outline: * even more on variant calling * even more on snakemake * discuss "real" variant calling on big genomes (GATK, etc.) ## Learning goals * Start using farm, github, and conda. * Learn about default rules. * Learn about wildcards. ## Day 3: More variant calling with more snakema

--- tags: ggg, ggg2020,ggg298 --- [toc] # GGG 298, jan 2020 - Week 3 - conda for software installation! Titus Brown and Shannon Joslin, Jan 22, 2020 Learning objectives: * learn the basics of software installation, software dependencies, and isolation environments * learn about conda and how to use it * learn about bioconda and how to use it Other references: * [ANGUS 2019 lesson](https://angus.readthedocs.io/en/2019/conda_tutorial.html) * [Why you need Python Environments and How to Manage

--- tags: ggg, ggg2020, ggg298 --- # GGG 298, Jan 2020 - Week 4 - snakemake for running workflows! [toc] ## Side note I'm available for office hours today, in CCAH 251 or 253. Shannon Office Hours: Friday 11am-12pm in the DataLab (3rd Floor Library) ## Learning objectives By the end of this lecture, students will: * know how to make basic workflows in snakemake rules * understand variable substitution in snakemake rules * understand wildcard matching in snakemake rules * be introduced to

--- tags: ggg, ggg2020, ggg298 --- # GGG 201(b), Lab Homework 1 Due at the beginning of class on Friday, 1/31. ## 1. Sign up for GitHub Classroom Sign up for GitHub Classroom using https://classroom.github.com/a/VoyiLDCW. This will probably involve creating a (free) GitHub account. ## 2. Log into farm & clone your github repo for hw1 On farm, clone your assignment repository, which will be something like `https://github.com/dib-lab/2020-ggg-201b-lab-hw1-ctb`; do so like this, ``` git clone

[toc] # Recruiting postdocs for biomedical data science training! (Posted January 14th, 2020.) The Lab for Data Intensive Biology at UC Davis is seeking to hire multiple postdocs for a biomedical data science training project. These NIH-funded postdocs will spearhead development of pilot workshop and training materials for multiple NIH Common Fund projects, with the goal of improving data use and reuse by training biomedical researchers and clinicians in cloud-based data analysis. (See links b

# GGG 201(a) 2019 - class 1 - NOTES Titus Brown, ctbrown@ucdavis.edu ## A very brief intro Modern sequencing data analysis relies on a fairly standard set of data science approaches. I'm going to slowly walk through a particular RNAseq workflow and show you how things work. This will be a brief intro to the basic concepts that we'll explore more thoroughly in the GGG 201(b) labs. If you feel completely overwhelmed - never fear! This is a much faster introduction than we do in 201(b), when we