Matches in Nanopublications for { ?s <http://schema.org/description> ?o ?g. }
- f8b3510c-35aa-4492-89bb-b108b506749d description "Copernicus Atmosphere Monitoring Service PM2.5, 2 day forecasts, 24th December 2021 at 12:00 UTC" assertion.
- zenodo.5805953 description "Dataset used in the Galaxy Pangeo tutorials on Xarray. Data is in netCDF format and is from Copernicus Air Monitoring Service and more precisely PM2.5 (Particle Matter < 2.5 μm) 4 days forecast from December, 22 2021. This dataset is very small and there is no need to parallelize our data analysis. Parallel data analysis with Pangeo is not covered in this tutorial and will make use of another dataset." assertion.
- zenodo.6399102 description "This is a tarball for the Docker Galaxy pangeo-JupyterLab image - Version 1c0f66b. To use it: download the image file docker-pangeo-notebook-1c0f66b.tar load it with docker with the command: docker load --input docker-pangeo-notebook-1c0f66b.tar launch the Docker container binding of your data folder (on the local machine) with the /import folder i(inside the container) with the command: docker run -v my_data_folder:/import -p 7777:8888 quay.io/nordicesmhub/docker-pangeo-notebook:1c0f66b start your favorite web browser and go to: http://localhost:7777/ipython/ See https://github.com/NordicESMhub/docker-pangeo-notebook for more details" assertion.
- tutorial.html description "Training material (hands-on) where Pangeo Notebook is used to learn Xarray. This training is part of the Galaxy Training Network (GTN). In this tutorial, we will learn about Xarray, one of the most used Python library from the Pangeo ecosystem. We will be using data from Copernicus Atmosphere Monitoring Service and more precisely PM2.5 (Particle Matter < 2.5 μm) 4 days forecast from December, 22 2021. Parallel data analysis with Pangeo is not covered in this tutorial." assertion.
- docker-climate-notebook description "This github repository contains all the sources required for building the docker containers that are made available in Quay Container Registry." assertion.
- docker-climate-notebook description "This github repository contains all the sources required for building the docker containers that are made available in Quay Container Registry." assertion.
- cb869c7a-7a89-49dd-9038-b8a05a91dc6e description "🐳 🔬 📚 Jupyter running in a docker container. This image can be used to integrate Jupyter into Galaxy. This Jupyter Docker container is used by the Galaxy Project and can be installed from the quay.io index (https://quay.io/repository/nordicesmhub/docker-climate-notebook)." assertion.
- a5017748-4c4f-4546-b555-4b1323fce016 description "Default Jupyter Notebook used when starting Galaxy Climate JupyterLab if no other Jupyter Notebook is passed by the user." assertion.
- c8a9d642-c401-43c4-9436-58f866edb277 description "This is the Galaxy Climate JupyterLab tool wrapper used by Galaxy to start the Galaxy Climate JupyterLab on a Galaxy instance." assertion.
- f974c6a2-5fb5-45ae-b19f-03968d55060f description "Most of the resources and information of this Research Object were created from this Jupyter Notebook." assertion.
- zenodo.4543739 description "By deploying JupyterLab with PANGEO, CESM and ESMValTool conda environments as a new Climate Galaxy interactive tool, we are aiming at bridging the gap between climate scientists and non-climate specialists. Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational research. One of the strength of Galaxy is that it does not require programming experience and allow researchers to easily upload data, run complex tools and workflows in a reproducible manner, and visualize results. Galaxy Climate is quite new and aims at offering tools to everyone interested in Climate Science so that they can analyse and visualize climate data produced by climate scientists. However, climate scientists and in particular climate modellers have very different working practices: they often like to use command lines for running climate models and thanks to the PANGEO community (a community platform for Big Data geoscience) the Jupyter ecosystem has become very popular with several deployments of JupyterHubs dedicated to climate data analysis. By deploying JupyterLab with PANGEO, CESM and ESMValTool conda environments as a new Climate Galaxy interactive tool (https://live.usegalaxy.eu/?tool_id=interactive_tool_climate_notebook), we are aiming at bridging the gap between climate scientists and non-climate specialists. On this poster, we will show typical use cases both for research (https://nordicesmhub.github.io/eosc-nordic-climate-demonstrator/02-use-cases/) and for teaching (https://nordicesmhub.github.io/NEGI-Abisko-2019/intro)." assertion.
- zenodo.4543739 description "By deploying JupyterLab with PANGEO, CESM and ESMValTool conda environments as a new Climate Galaxy interactive tool, we are aiming at bridging the gap between climate scientists and non-climate specialists. Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational research. One of the strength of Galaxy is that it does not require programming experience and allow researchers to easily upload data, run complex tools and workflows in a reproducible manner, and visualize results. Galaxy Climate is quite new and aims at offering tools to everyone interested in Climate Science so that they can analyse and visualize climate data produced by climate scientists. However, climate scientists and in particular climate modellers have very different working practices: they often like to use command lines for running climate models and thanks to the PANGEO community (a community platform for Big Data geoscience) the Jupyter ecosystem has become very popular with several deployments of JupyterHubs dedicated to climate data analysis. By deploying JupyterLab with PANGEO, CESM and ESMValTool conda environments as a new Climate Galaxy interactive tool (https://live.usegalaxy.eu/?tool_id=interactive_tool_climate_notebook), we are aiming at bridging the gap between climate scientists and non-climate specialists. On this poster, we will show typical use cases both for research (https://nordicesmhub.github.io/eosc-nordic-climate-demonstrator/02-use-cases/) and for teaching (https://nordicesmhub.github.io/NEGI-Abisko-2019/intro)." assertion.
- zenodo.6394185 description "This is a tarball for the Docker climate-JupyterLab image - Version 2021-03-18. To use it: download the image file docker-climate-notebook-2021-03-18.tar load it with docker with the command: docker load --input docker-climate-notebook-2021-03-18.tar launch the Docker container binding of your data folder (on the local machine) with the /import folder i(inside the container) with the command: docker run -v my_data_folder:/import -p 7777:8888 quay.io/nordicesmhub/docker-climate-notebook:2021-03-18 start your favorite web browser and go to: http://localhost:7777/ipython/ See https://github.com/NordicESMhub/docker-climate-notebook for more details" assertion.
- zenodo.6394185 description "This is a tarball for the Docker climate-JupyterLab image - Version 2021-03-18. To use it: download the image file docker-climate-notebook-2021-03-18.tar load it with docker with the command: docker load --input docker-climate-notebook-2021-03-18.tar launch the Docker container binding of your data folder (on the local machine) with the /import folder i(inside the container) with the command: docker run -v my_data_folder:/import -p 7777:8888 quay.io/nordicesmhub/docker-climate-notebook:2021-03-18 start your favorite web browser and go to: http://localhost:7777/ipython/ See https://github.com/NordicESMhub/docker-climate-notebook for more details" assertion.
- climate-jupyter-galaxy_web.gif description "This is a gif animated image showing how to start the Galaxy Climate JupyterLab in Galaxy Europe" assertion.
- climate-jupyter-galaxy_web.gif description "This is a gif animated image showing how to start the Galaxy Climate JupyterLab in Galaxy Europe" assertion.
- map_vis_Galaxy.gif description "This is a gif animated image showing some of the functionalities of the Galaxy Climate JupyterLab" assertion.
- map_vis_Galaxy.gif description "This is a gif animated image showing some of the functionalities of the Galaxy Climate JupyterLab" assertion.
- docker-climate-notebook description "These docker images (different tags) correspond to the docker images built for Galaxy Climate JupyterLab. The docker images can be used within Galaxy and as standalone docker images. You can use the same images we use in Galaxy on your local computer or any other platform: 1. Pull an existing image locally docker pull quay.io/nordicesmhub/docker-climate-notebook 2. Run a pre-build image from docker registry 3. To start your JupyterLab: docker run -p 7777:8888 quay.io/nordicesmhub/docker-climate-notebook and you will top open a new terminal and start your favorite web browser. your running Jupyter Notebook instance on http://localhost:7777/ipython/. Remark: for reproducibility purpose, we suggest you use a specific tag e.g. docker pull quay.io/nordicesmhub/docker-climate-notebook:2021-03-18 Then use the same tag when starting your JupyterLab application: docker run -p 7777:8888 quay.io/nordicesmhub/docker-climate-notebook:2021-03-18" assertion.
- docker-climate-notebook description "These docker images (different tags) correspond to the docker images built for Galaxy Climate JupyterLab. The docker images can be used within Galaxy and as standalone docker images. You can use the same images we use in Galaxy on your local computer or any other platform: 1. Pull an existing image locally docker pull quay.io/nordicesmhub/docker-climate-notebook 2. Run a pre-build image from docker registry 3. To start your JupyterLab: docker run -p 7777:8888 quay.io/nordicesmhub/docker-climate-notebook and you will top open a new terminal and start your favorite web browser. your running Jupyter Notebook instance on http://localhost:7777/ipython/. Remark: for reproducibility purpose, we suggest you use a specific tag e.g. docker pull quay.io/nordicesmhub/docker-climate-notebook:2021-03-18 Then use the same tag when starting your JupyterLab application: docker run -p 7777:8888 quay.io/nordicesmhub/docker-climate-notebook:2021-03-18" assertion.
- 64aee73b-a05c-433f-bbf7-2ed35ec42601 description "Collection and analysis of satellite data to monitor the effects of COVID-19 lockdown on water clarity in the north Adriatic Sea" assertion.
- 47de04b7-3e7d-48ef-b79a-bee388d95a56 description "Satellite data on Chl-a and Kd490" assertion.
- 662ddab9-0d68-4808-b2de-6dcdda1adbd5 description "Results" assertion.
- 6a9dd591-fc94-41f6-b1c8-9a0498329c69 description "Discover, subset, download and visualize satellite data stored in a Data Cube from the ADAM Platform" assertion.
- 0bede41c-0982-459d-bf19-40125ce14de6 description "Discover and subset satellite data from the ADAM Platform" assertion.
- abe41c35-f2eb-411a-8fb0-d5eee9a27d7b description "Satellite data on water clarity in the Venice Lagoon during the COVID 19 lockdown" assertion.
- 15e9432f-53ee-4ea8-b1a3-6fdcaca7cf9e description "Collection and analysis of satellite data to monitor the effects of COVID-19 lockdown on water clarity in the north Adriatic Sea" assertion.
- 499ad5e0-87a2-4eb8-a4e9-4f36dde18085 description "Discover, subset, download and visualize satellite data stored in a Data Cube from the ADAM Platform" assertion.
- 7a81856f-ea74-465a-ad3c-9d45e39d7da4 description "Results" assertion.
- e46c4797-f9e9-409b-9ba9-12f6d88bd37b description "Satellite data on Chl-a and Kd490" assertion.
- 782bfaab-da7e-425a-ad09-51a01e156155 description "Satellite data on water clarity in the Venice Lagoon during the COVID 19 lockdown" assertion.
- 8cfd02af-82ac-46c7-af65-65f6f7e40f91 description "Discover and subset satellite data from the ADAM Platform" assertion.
- conda-linux-64.lock description "Lock conda file for linux-64 OS of the Jupyter notebook hosted by the Environmental Data Science Book" assertion.
- conda-osx-64.lock description "Lock conda file for osx-64 OS of the Jupyter notebook hosted by the Environmental Data Science Book" assertion.
- requirements.txt description "Pip requirements file containing libraries to install after conda lock" assertion.
- 94486a7f-e046-461f-bbb9-334ec7b57040 description "The research object refers to the Tree crown delineation using detectreeRGB notebook published in the Environmental Data Science book." assertion.
- environment.yml description "Conda environment when user want to have the same libraries installed without concerns of package versions" assertion.
- notebook.ipynb description "Jupyter Notebook hosted by the Environmental Data Science Book" assertion.
- notebook.html description "Rendered version of the Jupyter Notebook hosted by the Environmental Data Science Book" assertion.
- DIAM description "Private Github repository containing the source code for DIAM economic model." assertion.
- e05b90f7-5c22-4741-8b27-c43f5a5d70b4 description "This Research Object is related to the work on the coupling of the Norwegian Earth System Model with DIAM economic model to explore the economic impact of climate change." assertion.
- f55e746b-6a1e-4712-ac21-a3c99869783d description "🐳 🔬 📚 Jupyter running in a docker container. This image can be used to integrate Jupyter into Galaxy. This Jupyter Docker container is used by the Galaxy Project and can be installed from the quay.io index (https://quay.io/repository/nordicesmhub/docker-climate-notebook)." assertion.
- 1ed42fe1-b9ab-45aa-93fa-e4711e59ee46 description "This is the Galaxy Climate JupyterLab tool wrapper used by Galaxy to start the Galaxy Climate JupyterLab on a Galaxy instance." assertion.
- c478e527-cbca-4660-b2fa-cbfc9124b7d6 description "Most of the resources and information of this Research Object were created from this Jupyter Notebook." assertion.
- c54e557e-c1b7-4964-9989-9261fe5fd80c description "Default Jupyter Notebook used when starting Galaxy Climate JupyterLab if no other Jupyter Notebook is passed by the user." assertion.
- f84d00ef-47b2-40b3-af26-099ed7e82f5b description "<p>This research object, was created in order to further analyse and interpret the results from the research object http://sandbox.rohub.org/rodl/ROs/HD_chromatin_analysis/ (HD chromatin analysis). The workflows in this research object are using the anni web services, implemented by the Biosemantics group.</p>" assertion.
- 2ea2f7b6-1c15-454f-b62a-e7656bb81db4 description "This workflow lists all IDs and descriptions of the predefined concept set" assertion.
- 473e57ab-4056-427a-a8d9-b2c62e9b34d4 description "This workflow takes two concept ids as input and returns the top ranking "B" concepts according to Swanson's ABC model of discovery, where the relationships AB and BC are known and reported in the literature, and the implicit relationship AC is a putative new discovery. It might also be the case that AC is already known. In that case AC does not represent a new discovery but will still be returned (see workflow example values). The B concepts are returned sorted on the percentage of the contributions of the individual concepts to the coherence score (the average of the inner product scores of all possible concept pairs within the group). This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery." assertion.
- 7f5b48a1-083d-4891-b311-b4627ceaa7ab description "This workflow annotates a comma separated gene list with a predefined concept set as for example Biological processes or Disease/syndrome. To obtain the particular id for each concept set (e.g. "5" for Biological processes), the workflow listPredefinedConceptSets needs to run first. The workflow is using the anni web services" assertion.
- 840546e9-eecd-455e-b3f7-b1893b29e083 description "This workflow can prioritize genes that are related to a specific concept, e.g. HTT. In order to obtain the concept id of the term that is going to be matched against the gene list, the workflow Get concept suggestions from term, needs to run first. matchConceptProfileList: the gene list we want to match (order) against a particular concept queryConceptProfileList: the concept (or gene list) we want to match the query against" assertion.
- cb796e52-689f-4e9e-8842-09612588af02 description "Sketch of the workflows and their explanation, for data interpretation, plus the connection to the output from the RO for chromatin analysis" assertion.
- ccd9b022-3e2d-422b-a5c5-1e12af73b5c7 description "This workflow suggests concept ids that match the query term. The user can run this workflow with any term of interest as for example "human", "htt", "Transcription" etc, and will get suggestions for concept ids together with descriptions. Then can choose the concept id that matches the best to her/his needs and use it to the rest of the CPA workflows" assertion.
- 2e023e94-f276-4281-8a0d-45568bb3755c description "Application of SOAP2denovo2 to the S. Aureus genome assembly" assertion.
- 8d28fd47-26d3-4831-8287-b768a6bfafe6 description "Galaxy workflow for reproducing Table 2 of SOAPdenovo paper" assertion.
- 7b766778-d12f-45b3-bb71-ab4e95cbbc2c description "The SOAPdenovo2 case study is a reproducibility study aimed at exploring how existing data models and workflow enactment engines can help assess, record and preserve scientific workflows and associated findings by reviewing a comparison between sequence assembly algorithm performance in the light of development of the <a href="http://www.gigasciencejournal.com/content/1/1/18">SOAPdenovo2 de novo genome assembler</a>. The case study was a joint effort by the <a href="http://www.gigasciencejournal.com/">GigaScience journal</a>, the <a href="http://isacommons.org/"> Investigation/Study/Assay</a> (ISA), <a href="http://nanopub.org/">Nanopublication</a> (Nanopub) and <a href="http://researchobject.org/">Research Object</a> (RO) communities and SOAPdenovo2 de novo genome assembler developers. See source: <a href="http://isa-tools.github.io/soapdenovo2/">http://isa-tools.github.io/soapdenovo2/</a>" assertion.
- 6e6dc2b6-2f66-4683-8a4f-53a4031b1013 description "This is the description" assertion.
- 7d9eb4a1-b374-414f-9812-e37bab4f4b39 description "Ground deformation mapping is a typical use case for this VRC. It may be carried out by different researchers on different volcanoes or even on the same volcano" assertion.
- 85dd9dc0-7231-454e-b3c6-ca619c8d4df2 description "Ground deformation mapping is a typical use case for this VRC. It may be carried out by different researchers on different volcanoes or even on the same volcano" assertion.
- fb83ce4a-bcbd-4708-984a-c67bdbc10bdd description "RO to facilitate development of early warning systems for natural hazards and their impacts within the UK." assertion.
- 94f3ec01-2fc1-4d36-9d33-df988345c96b description "This is a RO created for Land Monitoring Activities" assertion.
- 2d50b9a1-5eb8-46b2-a135-04c0db5da7e6 description "This is a RO created for Land Monitoring Activities" assertion.
- 81063ed1-cac7-4ef6-9e3b-21a2e134ebd2 description "This is a RO created for Land Monitoring Activities" assertion.
- 4d228be1-e395-4a7c-a8e4-a704a3556090 description "The Land Monitoring RO refers to the monitoring of urban, built-up and natural environments to identify certain features and anomalies or changes over areas of interest." assertion.
- 45a828a4-2697-44b1-aca4-c3a1a168cbeb description "The Land Monitoring RO refers to the monitoring of urban, built-up and natural environments to identify certain features and anomalies or changes over areas of interest." assertion.
- c237d670-e78c-4215-96a8-843b586d75da description "The Land Monitoring RO allows to monitor urban, built-up and natural environments in order to identify certain features and anomalies or changes over Areas of Interest." assertion.
- d18e59ae-ff07-4d59-a113-0202d37202aa description "The Land Monitoring RO allows to monitor urban, built-up and natural environments in order to identify certain features and anomalies or changes over Areas of Interest." assertion.
- eb7b6b9e-070d-45cc-a3e7-b71c7fe4cb08 description "In this RO we derive the MSFD indicator 1.5 (Habitat area) to assess the biological diversity descriptor. To do this in deep sea environment, the scientist (user) needs to implement a habitat suitability model." assertion.
- 96dc8341-f128-4c9c-b602-ce00010e76a0 description "Aggregation of the weekly official bulletin of September 2014. Attempt containing the PDFs" assertion.
- CoxBase description "First platform to combine all disparate genotyping systems for Coxiella burnetii" assertion.
- coxbase.q-gaps.de description "First platform to combine all disparate genotyping systems for Coxiella burnetii including MLVA, MST, IS1111, adaA and plasmid typing methods" assertion.
- coxbase.q-gaps.de description "First platform to combine all disparate genotyping systems for Coxiella burnetii including MLVA, MST, IS1111, adaA and plasmid typing methods" assertion.
- CoxBase description "First platform to combine all disparate genotyping systems for Coxiella burnetii" assertion.
- CoxBase description "First platform to combine all disparate genotyping systems for Coxiella burnetii" assertion.
- MLVAMethod description "High-resolution strain discrimination and comparison method based on tandem repeat analysis of 14 loci for Coxiella burnetii genotyping" assertion.
- __2 description "Tool for in silico extraction of MLVA amplicon lengths" assertion.
- MLVAMethod description "High-resolution strain discrimination and comparison method based on tandem repeat analysis of 14 loci for Coxiella burnetii genotyping" assertion.
- __2 description "Tool for in silico extraction of MLVA amplicon lengths" assertion.
- RAnh-o0GrvBfvoyiruq9UnbZOaNcHbue5O-FU6300R_Jg%23CoxiellaBurnetii description "Gram-negative, pleomorphic, obligate intracellular bacterium" assertion.
- RAnh-o0GrvBfvoyiruq9UnbZOaNcHbue5O-FU6300R_Jg%23QFever description "An infectious zoonotic disease" assertion.
- RAnh-o0GrvBfvoyiruq9UnbZOaNcHbue5O-FU6300R_Jg%23ValidationStudy description "Validation of CoxBase in silico genotyping implementation" assertion.
- RAnh-o0GrvBfvoyiruq9UnbZOaNcHbue5O-FU6300R_Jg%23InSilicoGenotyping description "Automated genotyping from genomic sequences using computational methods" assertion.
- RAnh-o0GrvBfvoyiruq9UnbZOaNcHbue5O-FU6300R_Jg%23InSilicoGenotyping description "Automated genotyping from genomic sequences using computational methods" assertion.
- kinetics-model description "Mathematical model describing transcript protection dynamics with RNase gradient treatment" assertion.
- kinetics-model description "Mathematical model describing RNA degradation dynamics using enzymatic kinetics" assertion.
- method description "Controlled Level of Contamination coupled to deep sequencing - a novel subcellular transcriptomics approach" assertion.
- method description "Controlled Level of Contamination coupled to deep sequencing - a novel subcellular transcriptomics approach" assertion.
- mock-coloc-experiment description "Control experiment with detergent-permeabilized membranes to detect false positives" assertion.
- mock-coloc-experiment description "Control experiment with detergent-permeabilized membranes to determine baseline RNase protection and validate method specificity" assertion.
- parameter-P0 description "Proportion of RNA protected from RNase degradation in the CoLoC-seq kinetics model" assertion.
- parameter-P0 description "Proportion of RNA protected from RNase digestion by organellar membranes" assertion.
- parameter-k-prime description "Pseudo-first-order rate constant describing RNA degradation velocity" assertion.
- parameter-k-prime description "Pseudo-first-order rate constant for RNA degradation by RNase" assertion.
- dataset-hek293 description "Transcriptome data from human Flp-In T-REx 293 cells" assertion.
- step-isolation description "Differential centrifugation of crude mitochondria" assertion.
- step-library-prep description "Selective sequencing of intact (non-RNase-cleaved) transcripts" assertion.
- advantage-kinetics-approach description "Tracks depletion dynamics across gradient instead of single RNase treatment" assertion.
- dataset description "776 sRNA annotations in Wikidata" assertion.
- deployment-toolforge description "Cloud infrastructure managed by Wikimedia Foundation providing hosting for InteractOA" assertion.
- sparql-arch description "Multi-step architecture translating user selections into executable SPARQL queries against Wikidata" assertion.
- sparql-arch description "The architecture consists of template definition, parameter binding, query composition, execution, result processing, and rendering steps" assertion.
