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followers: 24.0 following: 7.0 repos: 38.0 gists: 4.0

Name: Jayson Falkner

Type: User

Company: Google

Bio: Likes to build stuff

Location: Ann Arbor, MI

Blog: http://jaysonfalkner.com

Jayson Falkner's Projects

algorithms

Algorithms of interest and example usage in the real world.

bash-copypasta

Because you are using BASH to get stuff done and can't remember this syntax.

bonanza

Bonanza algorithm and source code from J. Proteome Res., 2008, 7 (11), pp 4614–4622 "A Spectral Clustering Approach to MS/MS Identification of Post-Translational Modifications"

cc2csv

Scala case class to CSV marshalling and unmarshalling. As simple as it gets.

choose-your-own-adventure

Simple choose your own adventure for teaching the basics of HTML and JavaScript

cloud-hpc-hackathon-2021

Cloud Hackathon for Arm-based HPC with AWS and Arm

devops

Some DevOps fun and a bootstrap of minimal, appropriate devops for the languages I've used.

efficient-django-queryset-use

Code and slides from Jayson's "Efficient Django QuerySet Use" presentation originally shown to The San Francisco Django Meetup Group and the Portland Python Users Group.

file_backed_logs

Simple file backed logging Scala API. Helpful for persisting data locally when you don't need all the dependencies and boilerplate associated with a database.

file_monitor

File monitoring API in Scala. Helpful for detecting additions to the file system and executing code once for new files or dirs.

find_image

A visual grep for finding 2D images in a larger image.

frag

MS/MS peptide fragmentation API. Useful for making combinations of post translatioal mofications and creating ion fragmentations.

github_project_management

Simple project management for engineering teams that rely on GitHub

MS/MS file readig and coversion API for .mgf, .pepXML, .t2d, .raw, and more. Falkner et al. Bioinformatics (2007) 23 (2): 262-263. "ProteomeCommons.org IO Framework: reading and writing multiple proteomics data formats"

jaf

MS/MS Java Analaysis Framework (JAF) with reference atomic weights, known stable isotopes, amino acid compositions, observed modifications of amino acids, and ion masses. Falkner et al. Bioinformatics 2006 "ProteomeCommons.org JAF: reference information and tools for proteomics."

lockfree

Thread safe, lock-free data structures in C using GCC's built-in atomics.

machine_learning

Artificial intelligence and machine learning examples, notes and docs.

metrics

A simple, Scala-based framework for extracting data and exporting it to JSON and/or CSV. Convenient for making data that Web/JS visualizations use or for users relying on tools such as JMP, R, Excel, etc.

metrics-bam-aligned

Metrics for aligned BAM files

metrics-cache

Scala-based cache for the metrics project.

metrics-docs

Searchable web UI based on static HTML/CSS/JS + ReactJS files. Makes it easy to quickly browse docs by namespace, tags or name matches.

metrics-examples

Examples for the Scala metrics repository

metrics-pbbam

Exports summary stats from PacBio's BAM specification: http://pacbiofileformats.readthedocs.io/en/3.0/BAM.html

metrics-pbbam-aligned

Exports alignment stats from PacBio's BAM specification: http://pacbiofileformats.readthedocs.io/en/3.0/BAM.html

metrics-sts

Exports PacBio's sts.xml format to JSON

metrics-subreadset

Exports PacBio's subreadset.xml format to JSON

nvidia-cuda-examples

NVIDIA CUDA examples for C and Rust

nvim

NeoVIM Configuration and Documentation

pfsm

MS/MS Peptide Finite State Machine (PFSM) source-code. Falkner et al. Bioinformatics. 2005 May 15;21(10):2177-84. Epub 2005 Mar 3. "Fast tandem mass spectra-based protein identification regardless of the number of spectra or potential modifications examined."

proteomecommons.org

Source-code for the now defunct ProteomeCommons.org website.

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