California Academy of Sciences, Institute for Biodiversity Science & Sustainability
Public repositories for IBSS projects
San Francisco
Pinned Repositories
antcat
World Catalog of Ants
antcolor
A research project to analyze ant coloration using data from AntWeb.org handled with Elasticsearch.
antweb
AntWeb is the world's largest online database of images, specimen records, and natural history information on ants. It is community driven and open to contribution from anyone with specimen records, natural history comments, or images.
BLATq
blatq is a modified version of BLAT—The BLAST-Like Alignment Tool to allow direct use of fastq files
cas-web-asset-server
Sample attachment server implementation for Specify.
COMB
C O M B
GItaxidIsVert
hyRADccg
Modified version of hyRAD, the protocol for hybridization capture using restriction site associated DNA (RAD) markers to create probes
minibar
Dual barcode and primer demultiplexing for MinION sequenced reads
RAxML_Astral_trees
This project generates Astral-III species trees from gene trees generated from RAxML using UCE data generated by the Phyluce pipeline. Then runs an Astral III analysis.
California Academy of Sciences, Institute for Biodiversity Science & Sustainability's Repositories
calacademy-research/minibar
Dual barcode and primer demultiplexing for MinION sequenced reads
calacademy-research/antcat
World Catalog of Ants
calacademy-research/antweb
AntWeb is the world's largest online database of images, specimen records, and natural history information on ants. It is community driven and open to contribution from anyone with specimen records, natural history comments, or images.
calacademy-research/COMB
C O M B
calacademy-research/antcolor
A research project to analyze ant coloration using data from AntWeb.org handled with Elasticsearch.
calacademy-research/cas-web-asset-server
Sample attachment server implementation for Specify.
calacademy-research/PythonLife
calacademy-research/web-asset-server
Sample attachment server implementation for Specify.
calacademy-research/assembly_etc
calacademy-research/Basic-R
A one script introduction to R from scratch
calacademy-research/CASES
calacademy-research/citations_finder
calacademy-research/load_analyzer
calacademy-research/picturae_csv_parser
stand alone program , used to QC csvs ready for specify import from picturae, nfn and digileap supplied data
calacademy-research/web-asset-importer
Image client used in conjunction with web-asset-server to process images/data into image server, and specify databases.
calacademy-research/bioawk.CAS
extensions to heng li's bioawk
calacademy-research/cas-dspace-dev
calacademy-research/ccgutils
utilties in various languages used in one or more projects
calacademy-research/Dalman_Twin_Microbiome_Scripts
Shell Scripts used in the Dalman et al. twin microbiome study
calacademy-research/HiFiMiTie
HiFiMiTie -- Find & Analyze Metazoan Mitochondria from HiFi reads
calacademy-research/collections_tools
A submodule storing util functions for use in ibss collections image server, data cleaning and data import related tasks
calacademy-research/color_finder
Can find % colors in image based on RGB or HSV values. Can be used for basic image sorting by color.
calacademy-research/expedition-clustering
calacademy-research/galapagos_island_mapper
calacademy-research/kompressor
finds and compresses large ascii files in parallel using pigz
calacademy-research/metadata_tools
utility package for writing and reading image metadata
calacademy-research/mySyntenyPortal
A stand-alone application for constructing websites for visualizing and browsing synteny blocks
calacademy-research/NASA-Project-3317
calacademy-research/publications_finder
A tool to aggregate institutional publications, powered by the OpenAlex API.
calacademy-research/webportal-installer
The Specify Web Portal