/awesome-coral-research

:ocean: A curated list of awesome coral research tools and resources.

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Awesome coral research Awesome DOI

An awesome list of resources that you can use in your coral research. Inspired by Awesome network analysis. Feel free to add any category and/or resource with a pull request. You can also contact me with your comments or suggestions.

Content:

Bleaching

Datasets

  • AGRRA data explorer: one of the largest database on Caribbean coral reef health indicators, with data available from more than 2,480 site surveys in 29 countries or territories throughout the Caribbean.
  • Cnidbase: Cnidarian evolution genomic database.
  • Allen Coral Atlas: High resolution satellite imagery and coral habitat maps to inform coral conservationMapping coral reefs to inform coral conservation.
  • Coral microbiome portal: Jump to Microbiology.
  • Coral reef imagery by Eileen Graham of Jamaica in the 1960s: Acollection of 1481 images that were made by Eileen Graham between 1966 and 1968 showing coral reefs from the northern coast of Jamaica.
  • Coral traits: A growing compilation of scleractinian coral life history trait, phylogenetic and biogeographic data.
  • Deep sea coral data porta: Deep sea coral and sponge data, images, and technical reports from research funded by NOAA’s Deep Sea Coral Research and Technology Program (DSCRTP) and its partners.
  • Fishbase: A global species database of fish species.
  • Coral transcriptomes: Jump to Genomics
  • OBIS: A global open-access data and information clearing-house on marine biodiversity for science, conservation and sustainable development.
  • Venezuelan transects: A photographic data set of reef and coral communities across Venezuela.

Data analysis

  • R: A language and environment for statistical computing and graphics.
  • RStudio: An integrated development environment for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.

Data and project management

Education

Enzymatic assays

  • BRENDA: Enzymatic information system.

Epizootiology

  • Caribbean Coral Disease Watch: Online tool to enhance collaboration, streamline data collecting and sharing in the Caribbean and better track disease outbreaks, mainly those that resemble Scleractinian Coral Tissue Loss Disease.
  • CoDiRNet: Coral Disease Research Network, a repository compiling papers about coral diseases, with focus on affected genera, ecoregions, and research questions.
  • Collecting corals for histopathology. A practical guide: Jump to Histology
  • Coral Disease and Health Workshop: Coral Histopathology II: Jump to Histology
  • Virgin Islands Coral Disease: A repository with information about stony coral tissue loss disease (SCTLD) epidemiology, research, intervention, and more that is being conducted in the Virgin Islands territories.

Funding

  • Coral Reef Funding Landscape: A tool exploring international funding allocations for the sustainable management of coral reefs and related mangroves and seagrass ecosystems.
  • Open Grants: A list of openly-shared grant proposals. The authors do this to open up science so that all stages of the process can benefit from better interaction and communication and to provide examples for early career scientists writing grants.

Genomics

Histology

Identification and Taxonomy

Image annotation

  • Biigle: BIIGLE is a web service for the efficient and rapid annotation of still images and videos. It was built for marine environmental monitoring and exploration but can be used for any image annotation task.
  • BioDock.ai: Web-based Deep-AI assisted image annotation tool.
  • CATAMI Classification scheme: Standard classification scheme for scoring marine biota and physical characteristics from underwater imagery.
  • CoralNet: A web solution for coral reef analysis. Upload coral reef images, organize and annotate images, and view annotation statistics.
  • CPCe: A tool for the determination of coral cover using transect photographs. Only compatible with Windows.
  • Seascape: A free software program to get semi-automatically segmented images (homogenous regions) from underwater photographs of benthic communities, where each individual patch (species/categories) is routinely associated to its area cover and perimeter.
  • Photoquad: A free software for advanced image processing of 2D photographic quadrat samples, dedicated to ecological applications. The system is designed to integrate all major 2D base analyses used in marine biology and ecology for studying biodiversity of sessile communities through photographic sampling.
  • Squidle: Online and in-field platforms for exploration, management, and annotation of georeferenced images & video.
  • TagLab: AI-powered segmentation software designed to support the analysis of large orthographic images generated through the photogrammetric pipeline.

Microbiology:

  • Coral microbiome database: A custom ARB database of SSU rRNA gene sequences from corals, as well representative cultivated and environmental sequences from public sources.
  • Coral microbiome portal: Database that brings together next generation sequencing data of coral-associated microorganisms from studies conducted thoughout the world’s reefs.
  • NetShift:a methodology and web app for understanding driver microbes from healthy and disease microbiome datasets.

Paleobiology:

  • Paleobiology database: a public database of paleontological data that anyone can use, maintained by an international non-governmental group of paleontologists.

Paper discovery and access

  • Dimensions: Search engine that integrates information about grants, publications, citations, clinical trials and patents in one place.
  • Meta: Tool that helps researchers discover scientific literature using AI.
  • Open access button: Free, legal research articles and data delivered instantly or automatically requested from authors.
  • Peerus: A scientific monitoring platform that will provide the latest publications of your interest in real time.
  • Unpaywall: browser extension that automatically checks its open database of legal, open-access articles. If there's an open version somewhere, you'll see a green tab on the article.

Presentations

  • Bioicons: A free library of open source icons for scientific illustrations using vector graphics software such as Inkscape or Adobe Illustrator.
  • Biorender: Thousands of scientific icons, mostly related to genetics and biochemistry.
  • IAN media library: The IAN symbol libraries contain over 3000 custom made vector symbols designed specifically for enhancing science communication products with diagrammatic representations of complex processes. You can download them individually, or as an entire package in AI, SVG, or PNG formats.
  • PhyloPic: Free silhouette images of animals, plants, and other life forms.

Protocols sharing and discovery

  • Protocols.io: An open access platform for sharing and discovering up-to-date life science methods. Discover corrections and optimizations of the methods you use; share and get credit for your knowledge
  • Scientific protocols: An open access platform for sharing and discovering protocols and methods. The site is heavily focused on GitHub integration.

Restoration

Scientific writing

  • Authorea: An online collaborative writing tool that allows researchers to write, cite, collaborate, host data and publish. It also supports an online LaTeX editor as well as a Markdown (wiki) editor.
  • CRediT: CRediT is high-level taxonomy, including 14 roles, that can be used to represent the roles typically played by contributors to scientific scholarly output. The roles describe each contributor’s specific contribution to the scholarly output.
  • Manuscripts: An online free tool for writing scientific documents.
  • Overleaf: An online LaTeX and Rich Text collaborative writing and publishing tool that makes the whole process of writing, editing and publishing scientific documents much quicker and easier.
  • Texture: Texture is an open-source toolset for the production of scientific content.
  • Stencila: Stencila provides a set of open-source software components enabling reproducible research within the tool of your choice. Stencila allows you to write reproducible documents containing interactive source code using the interfaces you are most familiar with. Stencila components can be combined in various ways and plugged into existing reproducible infrastructure.

Structure-from-Motion and related

  • Agisoft Photoscan: a stand-alone software product that performs photogrammetric processing of digital images and generates 3D spatial data. Proprietary software.
  • Bundler: A structure-from-motion (SfM) system for unordered image collections.
  • Hugin: Stitching any series of overlapping pictures.
  • Meshlab: Open source system for processing and editing 3D triangular meshes.
  • Meshroom Open-source 3D Reconstruction Software based on the AliceVision Photogrammetric Computer Vision framework.
  • Sketchfab: Publish and find 3D models online.
  • OpenCV SfM module: The opencv_sfm module contains algorithms to perform 3d reconstruction from 2d images.
  • OpenDroneMap: Generate maps, point clouds, 3D models and DEMs from drone, balloon or kite images.
  • OpenMVG: OpenMVG (Multiple View Geometry) is a library for computer-vision scientists and targeted for the Multiple View Geometry community.
  • VisualSFM: A GUI application for 3D reconstruction using structure from motion (SFM).

Miscellanea

  • CaribNode: a regional information system that brings together authoritative data from national and regional entities, making it possible to create tools for resource management across the region.
  • CITES: Trade database: A database holding over 13 million records of trade in wildlife.
  • CITES: Checklist of species: The official list of CITES-listed species and the CITES appendix in which they are currently listed.
  • Coral-List: NOAA's listserver for coral reef information and news.
  • CoRIS: Coral reef information system. Portal that provides access to NOAA coral reef information and data products with emphasis on the U.S. states, territories and remote island areas.
  • CRESCYNT: Coral Reef Science and Cyberinfrastructure Network. A multi-tiered and multidisciplinary network of coral reef researchers, ocean scientists, cyberinfrastructure specialists, and computer scientists.
  • FathomNet: an open-source image database for understanding our ocean and its inhabitants
  • IUCN Red List of Threatened Species: A list providing taxonomic, conservation status and distribution information on plants, fungi and animals that have been globally evaluated using the IUCN Red List Categories and Criteria.
  • Mesophotic.org: A repository for information on mesophotic coral ecosystems
  • Reef base: A global information system for coral reefs.
  • Reefscape project: The Reefscape Project explores coral reefs at new biogeographic scales for science, conservation, management, and resource policy. The project is a multifaceted initiative combining extensive field work, high-tech remote sensing from the Carnegie Airborne Observatory and satellites, plus science communication and community outreach.

Acknowledgments

Thanks to the following colleagues (alphabetically listed) who have contributed with additions to this list: