{"id":2706,"date":"2018-01-17T10:06:36","date_gmt":"2018-01-17T10:06:36","guid":{"rendered":"https:\/\/www.swissfluxnet.ethz.ch\/?page_id=2706"},"modified":"2025-12-26T14:17:34","modified_gmt":"2025-12-26T13:17:34","slug":"links","status":"publish","type":"page","link":"https:\/\/swissfluxnet.ethz.ch\/index.php\/links\/","title":{"rendered":"Links"},"content":{"rendered":"<h1>Data Portals and Research Networks<\/h1>\n<ul>\n<li><strong><a href=\"https:\/\/www.icos-cp.eu\/\" target=\"_blank\" rel=\"noopener\">ICOS<\/a><\/strong>: The Integrated Carbon Observation System, ICOS, provides standardised and open data from close to 180 measurement stations across 16 European countries. The stations observe greenhouse gas concentrations in the atmosphere as well as carbon fluxes between the atmosphere, the land surface and the oceans. Thus, ICOS is rooted in three domains: Atmosphere, Ecosystem and Ocean.<\/li>\n<li><a href=\"https:\/\/www.icos-switzerland.ch\/\" target=\"_blank\" rel=\"noopener\"><strong>ICOS Switzerland<\/strong><\/a>: ICOS Switzerland is the Swiss contribution to the <a href=\"https:\/\/www.icos-cp.eu\/\" target=\"_blank\" rel=\"noopener\">Integrated Carbon Observation System Research Infrastructure ICOS RI<\/a> and is a cooperation of several research institutes<\/li>\n<li><strong><a href=\"https:\/\/data.icos-cp.eu\/\" target=\"_blank\" rel=\"noopener\">ICOS Data Portal<\/a><\/strong>: A centralized platform offering standardized greenhouse gas observations from the European-wide station network <a href=\"https:\/\/www.icos-cp.eu\/\" target=\"_blank\" rel=\"noopener\">ICOS<\/a>, with data released under a CC BY 4.0 license.<\/li>\n<li><a href=\"http:\/\/www.icos-etc.eu\/icos\/\" target=\"_blank\" rel=\"noopener noreferrer\"><strong>ICOS &#8211; Ecosystem Thematic Centre<\/strong><\/a>: This website host the ICOS Ecosystem Thematic Centre construction phase, providing all the information available and introducing the actual network of sites. The sections available on the top bar menu offer access to the documentation, working groups for protocols and demonstration experiment sites.<\/li>\n<li><strong><a href=\"http:\/\/fluxnet.fluxdata.org\/\" target=\"_blank\" rel=\"noopener noreferrer\">FLUXNET Data Portal<\/a>: <\/strong>Ecosystem fluxes from hundreds of sites.<\/li>\n<li><a href=\"https:\/\/ameriflux.lbl.gov\" target=\"_blank\" rel=\"noopener\"><strong>AmeriFlux Data Portal<\/strong>:<\/a> Standardized, quality-assured flux and meteo data from sites across the Americas.<\/li>\n<li><strong><a href=\"http:\/\/data.neonscience.org\" target=\"_blank\" rel=\"noopener\">NEON Data Portal<\/a><\/strong>: Provides access to consistent, continental-scale ecological data, including near real-time eddy covariance products available as early as five days post-collection.<\/li>\n<li><strong><a href=\"https:\/\/www.asiaflux.net\/\" target=\"_blank\" rel=\"noopener\">AsiaFlux Website<\/a><\/strong>: Serves as a regional research network for studying exchanges of carbon dioxide, water vapor, and energy between terrestrial ecosystems and the atmosphere in Asia.<\/li>\n<li><strong><a href=\"https:\/\/data.ozflux.org.au\/\" target=\"_blank\" rel=\"noopener\">OzFlux Data Portal<\/a><\/strong>: Part of the Australian Terrestrial Ecosystem Research Network (TERN), providing flux tower data collections for the Australasian region.<\/li>\n<li><a href=\"http:\/\/gaia.agraria.unitus.it\/\" target=\"_blank\" rel=\"noopener noreferrer\"><strong>EFDC &#8211; European Fluxes Database Cluster<\/strong><\/a>: Ecosystem fluxes from various research projects.<\/li>\n<li><strong><a href=\"https:\/\/www.japanflux.org\/index.php?page_id=0&amp;lang=english\" target=\"_blank\" rel=\"noopener\">JapanFlux<\/a>: <\/strong>JapanFlux is a network of scientists who belong to research groups that are involved in flux-related studies. A <a href=\"https:\/\/ads.nipr.ac.jp\/japan-flux2024\/\" target=\"_blank\" rel=\"noopener\">large-scale open dataset, &#8220;JapanFlux2024&#8221;<\/a> has been created in August 2025 (<a href=\"https:\/\/essd.copernicus.org\/articles\/17\/3807\/2025\/essd-17-3807-2025-discussion.html\" target=\"_blank\" rel=\"noopener\">paper<\/a>).<\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<h1>Software Tools and Code Repositories<\/h1>\n<ul>\n<li><a href=\"https:\/\/www.licor.com\/products\/eddy-covariance\/eddypro\" target=\"_blank\" rel=\"noopener\"><strong>EddyPro<\/strong><\/a><strong>:&nbsp;<\/strong><span class=\"notranslate\">Powerful open source (<a href=\"https:\/\/github.com\/LI-COR\/eddypro-engine\" target=\"_blank\" rel=\"noopener\">engine<\/a>, <a href=\"https:\/\/github.com\/LI-COR\/eddypro-gui\" target=\"_blank\" rel=\"noopener\">GUI<\/a>) application for processing eddy covariance data. It computes fluxes of water vapor (evapotranspiration), carbon dioxide, methane, other trace gases, and energy with the Eddy Covariance method. (<a href=\"https:\/\/amt.copernicus.org\/articles\/7\/2273\/2014\/\" target=\"_blank\" rel=\"noopener\">Fratini and Mauder, 2014<\/a>)<\/span><\/li>\n<li><a href=\"https:\/\/github.com\/bgctw\/REddyProc\" target=\"_blank\" rel=\"noopener\"><strong>REddyProc<\/strong><\/a>:&nbsp;R-package for eddy covariance data processing, e.g. gap-filling and partitioning of half-hourly data. (<a href=\"https:\/\/doi.org\/10.5194\/bg-15-5015-2018\" target=\"_blank\" rel=\"noopener\">Wutzler et al., 2018<\/a>)<\/li>\n<li><strong><a href=\"https:\/\/github.com\/fluxnet\/ONEFlux\" target=\"_blank\" rel=\"noopener\">ONEFlux Processing Suite<\/a><\/strong>: Open-source collection of codes used to standardize, gap-fill, and partition fluxes, compatible with the global FLUXNET2015 standard. (<a href=\"https:\/\/www.nature.com\/articles\/s41597-020-0534-3\" target=\"_blank\" rel=\"noopener\">Pastorello et al., 2020<\/a>)<\/li>\n<li><strong><a href=\"https:\/\/bitbucket.org\/juergenknauer\/bigleaf\/src\/master\/\" target=\"_blank\" rel=\"noopener\">bigleaf<\/a><\/strong>: R package for the calculation of physical (e.g. aerodynamic conductance, surface temperature) and physiological (e.g. canopy conductance, water-use efficiency) ecosystem properties from eddy covariance data and accompanying meteorological measurements. All calculations are based on a &#8216;big-leaf&#8217; representation of the vegetation and return representative bulk ecosystem\/canopy variables.<\/li>\n<li><strong><a href=\"https:\/\/footprint.kljun.net\/\" target=\"_blank\" rel=\"noopener\">Flux Footprint<\/a><\/strong>: A simple two-dimensional parameterisation for Flux Footprint Prediction (FFP) (<a href=\"https:\/\/gmd.copernicus.org\/articles\/8\/3695\/2015\/\" target=\"_blank\" rel=\"noopener\">Kljun et al, 2015<\/a>)<\/li>\n<li><a href=\"https:\/\/github.com\/AMF-FLX\/AMF-BASE-QAQC\" target=\"_blank\" rel=\"noopener\"><strong>AmeriFlux BASE QA\/QC Code<\/strong><\/a>: Python-based data-processing pipeline code used to assess data quality.<\/li>\n<li><a href=\"https:\/\/github.com\/icos-etc\/RFlux\" target=\"_blank\" rel=\"noopener\"><strong>RFlux Package<\/strong><\/a>: R-based graphical user interface for processing eddy covariance raw data (estimated through a call to the open source software EddyPro) and releasing high-quality GHG fluxes. Has been developed in the context of the <a href=\"http:\/\/www.icos-etc.eu\/icos\" target=\"_blank\" rel=\"noopener noreferrer\">ICOS Ecosystem Thematic Centre<\/a>. (<a href=\"https:\/\/bg.copernicus.org\/articles\/17\/1367\/2020\/\" target=\"_blank\" rel=\"noopener noreferrer\">Vitale et al., 2020<\/a>)<\/li>\n<li><a href=\"https:\/\/pypi.org\/project\/icoscp\/\" target=\"_blank\" rel=\"noopener\"><strong>ICOS Python Library (icoscp)<\/strong><\/a>: Library providing direct programmatic access to ICOS data objects, enabling researchers to load data files directly into memory.<\/li>\n<li><a href=\"https:\/\/cran.r-project.org\/web\/packages\/neonUtilities\/\" target=\"_blank\" rel=\"noopener\"><strong>neonUtilities R Package<\/strong><\/a>: Essential utilities for discovering, downloading, and stacking NEON data, including specialized functions for HDF5 eddy flux files.<\/li>\n<li><strong><a href=\"https:\/\/github.com\/lsigut\/openeddy\">openeddy<\/a><\/strong>: The openeddy package is a software infrastructure for eddy covariance data post-processing. It provides tools for handling data with attached metadata, setting up quality control scheme and summarizing and plotting the results. It is aligned with the <code>REddyProc<\/code> package that provides methods for uStar-filtering, gap-filling, and flux-partitioning. Thus the combined use of <code>openeddy<\/code> and <code>REddyProc<\/code> allows to run the whole eddy covariance post-processing chain.<\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<h1>Other Databases<\/h1>\n<ul>\n<li><a href=\"https:\/\/www.try-db.org\/TryWeb\/Home.php\" target=\"_blank\" rel=\"noopener noreferrer\"><strong>TRY &#8211; Plant Trait Database<\/strong><\/a>: Quantifying and scaling global plant trait diversity. 6.9 million trait records, 148,000 plant taxa, largely open access.<\/li>\n<li><strong><a href=\"http:\/\/www.fao.org\/soils-portal\/soil-survey\/soil-maps-and-databases\/harmonized-world-soil-database-v12\/en\/\" target=\"_blank\" rel=\"noopener noreferrer\">Harmonized World Soil Database<\/a>: <\/strong>30 arc-second raster database with over 15 000 different soil mapping units<\/li>\n<li><a href=\"http:\/\/european-webcam-network.net\/about_us.php\" target=\"_blank\" rel=\"noopener noreferrer\"><strong>EuroPhen &#8211; European Phenology Camera Network<\/strong><\/a>: Website that will help those interested in phenology to better understand the seasonal changes of different species.<\/li>\n<li><a href=\"https:\/\/www.earthsystemdatalab.net\/\" target=\"_blank\" rel=\"noopener noreferrer\"><strong>ESDL &#8211; Earth System Data Lab<\/strong><\/a>: The Earth System Data Lab (ESDL) seeks to be a service to the scientific community to greatly facilitate access and exploitation of multivariate data sets in Earth Sciences.<\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<h1>Programming<\/h1>\n<ul>\n<li><strong><a href=\"https:\/\/jupyter.org\/\">Jupyter notebook<\/a><\/strong>: Free software, open standards, and web services for interactive computing across all programming languages.<\/li>\n<li><strong><a href=\"https:\/\/docs.anaconda.com\/free\/miniconda\/index.html\">miniconda<\/a><\/strong>: a free minimal installer for conda. It is a small bootstrap version of Anaconda that includes only conda, Python, the packages they both depend on, and a small number of other useful packages (like pip, zlib, and a few others). If you need more packages, use the <code class=\"docutils literal notranslate\"><span class=\"pre\">conda<\/span> <span class=\"pre\">install<\/span><\/code> command to install from thousands of packages available by default in Anaconda\u2019s public repo, or from other channels, like conda-forge or bioconda.<\/li>\n<li><strong><a href=\"https:\/\/github.com\/pypa\/pipx\">pipx<\/a><\/strong>: Install and run Python applications in isolated environments.<\/li>\n<li><strong><a href=\"https:\/\/python-poetry.org\/\">Poetry<\/a><\/strong>: Python packaging and dependency management.<\/li>\n<li><strong><a href=\"https:\/\/www.python.org\/\">Python<\/a><\/strong>: Python is a programming language that lets you work quickly and integrate systems more effectively.<\/li>\n<li><strong><a href=\"https:\/\/www.r-project.org\/\">R<\/a><\/strong>: a free software environment for statistical computing and graphics.<\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<h1>Swiss FluxNet Hub<\/h1>\n<table style=\"border: 0px none #ffffff;\" border=\"0\" cellspacing=\"10\">\n<tbody>\n<tr>\n<td><a href=\"https:\/\/www.swissfluxnet.ethz.ch\/index.php\/hub\/\"><img decoding=\"async\" class=\"aligncenter wp-image-7694 lazyload\" data-src=\"https:\/\/www.swissfluxnet.ethz.ch\/wp-content\/uploads\/2020\/02\/icon_hub_sfn_20200209.jpg\" alt=\"\" width=\"150\" height=\"148\" src=\"data:image\/svg+xml;base64,PHN2ZyB3aWR0aD0iMSIgaGVpZ2h0PSIxIiB4bWxucz0iaHR0cDovL3d3dy53My5vcmcvMjAwMC9zdmciPjwvc3ZnPg==\" style=\"--smush-placeholder-width: 150px; --smush-placeholder-aspect-ratio: 150\/148;\"><\/a><\/td>\n<td style=\"text-align: left;\">&nbsp;<\/td>\n<td style=\"text-align: left;\"><strong><a href=\"https:\/\/www.swissfluxnet.ethz.ch\/index.php\/hub\/\" target=\"_blank\" rel=\"noopener noreferrer\">Swiss FluxNet Hub<\/a><\/strong><br \/>\nCollection of (often internal) links used by the SFN Team.<br \/>\n(Icon downloaded from <a href=\"https:\/\/commons.wikimedia.org\/wiki\/File:Wiki-tech-logo-hub.svg\" target=\"_blank\" rel=\"noopener noreferrer\">Wikimedia Commons<\/a>)<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Data Portals and Research Networks ICOS: The Integrated Carbon Observation System, ICOS, provides standardised and open data from close to 180 measurement stations across 16 European countries. The stations observe greenhouse gas concentrations in the atmosphere as well as carbon fluxes between the atmosphere, the land surface and the oceans. . . . <a class=\"readmore-link\" href=\"https:\/\/swissfluxnet.ethz.ch\/index.php\/links\/\">Read more<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":9,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"_lmt_disableupdate":"no","_lmt_disable":"no","ngg_post_thumbnail":0,"footnotes":""},"coauthors":[310],"class_list":["post-2706","page","type-page","status-publish","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/swissfluxnet.ethz.ch\/index.php\/wp-json\/wp\/v2\/pages\/2706","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/swissfluxnet.ethz.ch\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/swissfluxnet.ethz.ch\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/swissfluxnet.ethz.ch\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/swissfluxnet.ethz.ch\/index.php\/wp-json\/wp\/v2\/comments?post=2706"}],"version-history":[{"count":49,"href":"https:\/\/swissfluxnet.ethz.ch\/index.php\/wp-json\/wp\/v2\/pages\/2706\/revisions"}],"predecessor-version":[{"id":13388,"href":"https:\/\/swissfluxnet.ethz.ch\/index.php\/wp-json\/wp\/v2\/pages\/2706\/revisions\/13388"}],"wp:attachment":[{"href":"https:\/\/swissfluxnet.ethz.ch\/index.php\/wp-json\/wp\/v2\/media?parent=2706"}],"wp:term":[{"taxonomy":"author","embeddable":true,"href":"https:\/\/swissfluxnet.ethz.ch\/index.php\/wp-json\/wp\/v2\/coauthors?post=2706"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}