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gsg-kotlin

A search tool for GFE names of HLA and KIR genes.

https://github.com/kaeaton/gsg-kotlin

Science Score: 44.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
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    DOI references
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (3.3%) to scientific vocabulary

Keywords

bioinformatics gfe hla kir kotlin
Last synced: 11 months ago · JSON representation ·

Repository

A search tool for GFE names of HLA and KIR genes.

Basic Info
  • Host: GitHub
  • Owner: kaeaton
  • Language: Kotlin
  • Default Branch: main
  • Homepage:
  • Size: 486 KB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 7
  • Releases: 0
Topics
bioinformatics gfe hla kir kotlin
Created over 5 years ago · Last pushed over 2 years ago
Metadata Files
Readme Citation

README.md

GFE Search Generator

There are currently tens of thousands of known variants of the Human Leukocyte Antigen (HLA) genes, the genes most responsible for transplant success or failure, with new variants (known as “alleles”) being discovered and “named” every day. The current names give very little information about the structure of the proteins encoded by these genes, and in 2015, Dr. Steven Mack proposed a new naming convention called Gene Feature Enumeration (GFE). New tools are required to use the new GFE naming convention, including (1) the ability to switch between the HLA allele names and the GFE names, (2) search through the GFE names, and (3) assign GFE names to new alleles.

The project is built using Kotlin, JVM 17, OpenJavaFX 0.0.9, and TornadoFX, bundled together with Gradle.

Owner

  • Name: Katrina Eaton
  • Login: kaeaton
  • Kind: user
  • Location: Oakland, CA
  • Company: UCSF

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: GFE Search Generator
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Katrina
    family-names: Eaton
    email: katrina.eaton@ucsf.edu
    affiliation: 'University of California, San Francisco'
identifiers:
  - type: url
    value: 'https://github.com/kaeaton/GSG-Kotlin'
    description: >-
      The Gene Feature Enumeration (GFE) Search
      Generator
repository-code: 'https://github.com/kaeaton/GSG-Kotlin'
abstract: >-
  There are currently 24,009 known variants (alleles)
  of the Human Leukocyte Antigen genes, which are key
  to transplant success or failure, with new alleles
  being discovered and “named” every day. The current
  names give very little information about the
  structure of the proteins encoded by these genes,
  and, in 2015, Dr. Steven Mack proposed a new naming
  convention called Gene Feature Enumeration (GFE),
  designed to create machine-readable names. New
  tools are required to use the new GFE naming
  convention, including the ability to (1) switch
  between the allele names and the GFE names, (2)
  search across GFE names, and (3) assign GFE names
  to new alleles. In this thesis, I describe the GFE
  Search Generator, a tool designed to make allele
  identification using GFE names easier for research
  purposes. This will enable better matches between
  patients and donors for transplant purposes and
  will assist in research about autoimmune diseases.
keywords:
  - GFE
  - Gene Feature Enumeration
  - HLA
  - Human Leukocyte Antigen
  - KIR
  - Killer Immunoglobulin-like Receptor
  - Bioinformatics
license: GPL-3.0

GitHub Events

Total
Last Year

Issues and Pull Requests

Last synced: over 2 years ago

All Time
  • Total issues: 6
  • Total pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: 1 minute
  • Total issue authors: 1
  • Total pull request authors: 2
  • Average comments per issue: 0.67
  • Average comments per pull request: 0.33
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: 1 minute
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • kaeaton (6)
Pull Request Authors
  • kaeaton (2)
  • ghost (1)
Top Labels
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Dependencies

build.gradle.kts maven
  • com.beust:klaxon 5.5 implementation
  • com.fasterxml.jackson.module:jackson-module-kotlin 2.12.3 implementation
  • com.squareup.okhttp3:okhttp 4.9.1 implementation
  • com.squareup.okio:okio 2.10.0 implementation
  • io.github.java-diff-utils:java-diff-utils 4.11 implementation
  • io.ktor:ktor-client-cio 1.6.7 implementation
  • io.ktor:ktor-client-core 1.6.7 implementation
  • io.reactivex.rxjava3:rxkotlin 3.0.1 implementation
  • no.tornado:tornadofx 1.7.20 implementation
  • org.jetbrains.kotlin:kotlin-reflect 1.5.0 implementation
  • org.jetbrains.kotlinx:kotlinx-coroutines-core 1.5.2 implementation
  • org.jetbrains.kotlinx:kotlinx-serialization-json 1.2.2 implementation
  • com.nhaarman.mockitokotlin2:mockito-kotlin 2.2.0 testImplementation
  • org.junit.jupiter:junit-jupiter 5.7.0 testImplementation
  • org.junit.jupiter:junit-jupiter-engine 5.7.0 testImplementation
  • org.junit.jupiter:junit-jupiter-params 5.7.0 testImplementation
  • org.mockito:mockito-core 3.8.0 testImplementation
.github/workflows/codesee-arch-diagram.yml actions
  • Codesee-io/codesee-action v2 composite