New topic/tutorial: Materials science/uep tutorial

.github/labeler.yml

@@ -43,6 +43,8 @@ instructors:
   - topics/instructors/**/*
 introduction:
   - topics/introduction/**/*
+materials-science:
+  - topics/materials-science/**/*
 metabolomics:
   - topics/metabolomics/**/*
 metagenomics:

.github/workflows/docker-build.yaml

@@ -147,6 +147,19 @@ jobs:
         repository: galaxy/introduction-training
         tags: latest, 20.05
         dockerfile: topics/introduction/docker/Dockerfile
+  materials-science-docker:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Build and push to Docker Hub
+      uses: docker/build-push-action@v1
+      with:
+        username: ${{ secrets.docker_registry_username }}
+        password: ${{ secrets.docker_registry_password }}
+        registry: quay.io
+        repository: galaxy/materials-science-training
+        tags: latest, 20.05
+        dockerfile: topics/materials-science/docker/Dockerfile
   metabolomics-docker:
     runs-on: ubuntu-latest
     steps:

CODEOWNERS

@@ -22,8 +22,9 @@ topics/ecology/                    @galaxyproject/training-ecology
 topics/epigenetics/                @galaxyproject/training-epigenetics
 topics/galaxy-interface/           @galaxyproject/training-galaxy-ui @galaxyproject/training-galaxy-data-manipulation
 topics/genome-annotation/          @galaxyproject/training-genome-annotation
-topics/teaching/                @galaxyproject/training-instructors
+topics/teaching/                   @galaxyproject/training-instructors
 topics/introduction/               @galaxyproject/training-introduction
+topics/materials-science/          @galaxyproject/training-materials-science
 topics/metabolomics/               @galaxyproject/training-metabolomics
 topics/metagenomics/               @galaxyproject/training-metagenomics
 topics/proteomics/                 @galaxyproject/training-proteomics

CONTRIBUTORS.yaml

@@ -109,6 +109,12 @@ andrewjpage:
     orcid: 0000-0001-6919-6062
     joined: 2018-06
 
+
+anish-mudaraddi:
+    name: Anish Mudaraddi
+    email: [email protected]
+    joined: 2022-11
+
 andrewsnelgrove:
     name: Andrew Snelgrove
     joined: 2023-03
@@ -468,6 +474,12 @@ eancelet:
     joined: 2021-01
     elixir_node: fr
 
+elichad:
+    name: Eli Chadwick
+    email: [email protected]
+    orcid: 0000-0002-0035-6475
+    joined: 2022-11
+
 edmontosaurus:
     name: Edwin den Haas
     matrix: 'edmontosaurus:matrix.org'
@@ -807,6 +819,11 @@ jkreplak:
     joined: 2020-09
     orcid: 0000-0001-5563-1932
 
+joelvdavies:
+    name: Joel Davies
+    email: [email protected]
+    joined: 2022-11
+
 jontrow:
     name: Jon Trow
     joined: 2021-05
@@ -950,6 +967,11 @@ lamouresparus:
     twitter: lamouresparus
     joined: 2021-10
 
+leandro-liborio:
+    name: Leandro Liborio
+    email: [email protected]
+    joined: 2022-11
+
 Laura190:
     name: Laura Cooper
     email: [email protected]
@@ -1319,6 +1341,11 @@ RareSeas:
     name: Adelaide Rhodes
     joined: 2021-05
 
+patrick-austin:
+    name: Patrick Austin
+    email: [email protected]
+    joined: 2022-11
+
 paulineauffret:
     name: Pauline Auffret
     joined: 2022-08

metadata/materials-science.yaml

@@ -0,0 +1 @@
+../topics/materials-science/metadata.yaml

topics/materials-science/README.md

@@ -0,0 +1,5 @@
+
+Materials
+==========
+
+Please refer to the [CONTRIBUTING.md](../../CONTRIBUTING.md) before adding or updating any material

topics/materials-science/docker/Dockerfile

@@ -0,0 +1,26 @@
+
+# Galaxy - Materials
+#
+# to build the docker image, go to root of training repo and
+#    docker build -t materials-science -f topics/materials-science/docker/Dockerfile .
+#
+# to run image:
+#    docker run -p "8080:80" -t materials-science
+#    use -d to automatically dowload the datalibraries in the container
+
+FROM quay.io/bgruening/galaxy:20.05
+
+MAINTAINER Galaxy Training Material
+
+ENV GALAXY_CONFIG_BRAND "GTN: Materials"
+
+# copy the tutorials directory for your topic
+ADD topics/materials-science/tutorials/ /tutorials/
+
+# install everything for tutorials
+ADD bin/docker-install-tutorials.sh /setup-tutorials.sh
+ADD bin/mergeyaml.py /mergeyaml.py
+ADD bin/data_libarary_download.sh /data_libarary_download.sh
+RUN /setup-tutorials.sh
+
+ENTRYPOINT ["/data_libarary_download.sh"]

topics/materials-science/faqs/README.md

@@ -0,0 +1 @@
+../../../faqs/README.md

topics/materials-science/faqs/index.md

@@ -0,0 +1,3 @@
+---
+layout: faq-page
+---

topics/materials-science/index.md

@@ -0,0 +1,4 @@
+---
+layout: topic
+topic_name: materials-science
+---

topics/materials-science/metadata.yaml

@@ -0,0 +1,19 @@
+---
+name: materials-science
+type: use
+title: Materials Science
+summary: Modelling, simulation and analysis for the material science domain.
+docker_image: "quay.io/galaxy/materials-science-training"
+
+editorial_board:
+  - patrick-austin
+  - leandro-liborio
+
+requirements:
+  - type: internal
+    topic_name: introduction
+
+subtopics:
+  - id: muon-spectroscopy
+    title: "Muon Spectroscopy"
+    description: "These tutorials cover tools and workflows for muon spectroscopy."

topics/materials-science/slides/introduction.html

@@ -0,0 +1,71 @@
+---
+layout: introduction_slides
+logo: "GTN"
+title: Introduction to Muon Spectroscopy
+type: introduction
+contributions:
+  authorship:
+    - anish-mudaraddi
+    - elichad
+    - patrick-austin
+    - leandro-liborio
+  editing:
+    - joelvdavies
+  funding:
+    - eurosciencegateway
+subtopic: muon-spectroscopy
+priority: 1
+---
+
+# What are "Muons"?
+
+Muons are subatomic particles that have spin 1/2, carry one elementary electric
+charge, and have a mass about 207 times the rest mass of the electron or 1/9th
+of the rest mass of the proton.
+
+Muons may be though of as "heavy electrons" or "light protons", and they are
+generated via nuclear reactions currently at four muon sources around the world.
+
+The ISIS Neutron and Muon Source, at the Rutherford Appleton Laboratory in the
+UK, is one of them. 
+
+---
+
+# What is Muon Spectroscopy?
+
+In a muon experiment, the muons are channelled into beamlines and fired towards
+the samples that we want to study.
+
+They are implanted into the sample and decay with an average lifetime of 2.2μs,
+releasing a positron in the direction of the spin of the muon at the time of
+decay.
+
+The positrons leave the sample and are collected by a positron detector. These
+detections are used to infer the behaviour of the muons and, with that, study
+different properties of the sample. 
+
+![Diagram showing muon implantation, decay, and positron detection](../images/muon_spectroscopy_diagram.png)
+---
+
+# Muon Simulations
+
+One of the main problems in Muon Spectroscopy is knowing where the muon is
+implanted - where it stops - inside the sample.  
+
+The stopping site is influenced by many factors and knowing its location is very
+useful for the interpretation of muon experiments.
+
+Computer simulations can help with estimating the muon stopping site.
+
+---
+
+# Muon Galaxy tools
+
+Muon Galaxy gives easy access to a set of software tools developed by the 
+[Muon Spectroscopy Computational Project (MSCP)](https://muon-spectroscopy-computational-project.github.io/index.html)
+for simulating muon science experiments including:
+
+  - approximating the muon stopping site
+
+  - simulating spin dynamics of muonated structures
+

topics/materials-science/tutorials/muon-stopping-sites-muairss-uep/data-library.yaml

@@ -0,0 +1,27 @@
+---
+destination:
+  type: library
+  name: GTN - Material
+  description: Galaxy Training Network Material
+  synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org
+items:
+- name: Materials Science
+  description: Modelling, simulation and analysis for the material science domain.
+  items:
+  - name: Finding muon stopping sites using the UEP and AIRSS methods
+    items:
+    - name: 'DOI: 10.5281/zenodo.6344385'
+      description: latest
+      items:
+      - url: https://zenodo.org/record/6344385/files/Si.cell
+        src: url
+        ext: cell
+        info: https://zenodo.org/record/6344385
+      - url: https://zenodo.org/record/6344385/files/Si.castep
+        src: url
+        ext: castep
+        info: https://zenodo.org/record/6344385
+      - url: https://zenodo.org/record/6344385/files/Si.den_fmt
+        src: url
+        ext: den_fmt
+        info: https://zenodo.org/record/6344385

topics/materials-science/tutorials/muon-stopping-sites-muairss-uep/tutorial.bib

@@ -0,0 +1,76 @@
+
+# This is the bibliography file for your tutorial.
+#
+# To add bibliography (bibtex) entries here, follow these steps:
+#  1) Find the DOI for the article you want to cite
+#  2) Go to https://doi2bib.org and fill in the DOI
+#  3) Copy the resulting bibtex entry into this file
+#
+# To cite the example below, in your tutorial.md file
+# use {% cite Batut2018 %}
+#
+# If you want to cite an online resourse (website etc)
+# you can use the 'online' format (see below)
+#
+
+@software{Sturniolo_pymuon-suite_2022,
+  author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and Mudaraddi, Anish and {Muon Spectroscopy Computational Project}},
+  license = {GPL-3.0},
+  month = {8},
+  title = {{pymuon-suite}},
+  url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite},
+  version = {v0.2.3},
+  year = {2022}
+}
+
+@article{Liborio2018,
+  doi = {10.1063/1.5024450},
+  url = {https://doi.org/10.1063/1.5024450},
+  year = {2018},
+  month = apr,
+  publisher = {{AIP} Publishing},
+  volume = {148},
+  number = {13},
+  pages = {134114},
+  author = {Leandro Liborio and Simone Sturniolo and Dominik Jochym},
+  title = {Computational prediction of muon stopping sites using <i>ab initio</i> random structure searching ({AIRSS})},
+  journal = {The Journal of Chemical Physics}
+}
+
+@article{Sturniolo2019,
+  doi = {10.1063/1.5085197},
+  url = {https://doi.org/10.1063/1.5085197},
+  year = {2019},
+  month = apr,
+  publisher = {{AIP} Publishing},
+  volume = {150},
+  number = {15},
+  pages = {154301},
+  author = {Simone Sturniolo and Leandro Liborio and Samuel Jackson},
+  title = {Comparison between density functional theory and density functional tight binding approaches for finding the muon stopping site in organic molecular crystals},
+  journal = {The Journal of Chemical Physics}
+}
+
+@article{Sturniolo2020,
+  doi = {10.1063/5.0012381},
+  url = {https://doi.org/10.1063/5.0012381},
+  year = {2020},
+  month = jul,
+  publisher = {{AIP} Publishing},
+  volume = {153},
+  number = {4},
+  pages = {044111},
+  author = {Simone Sturniolo and Leandro Liborio},
+  title = {Computational prediction of muon stopping sites: A novel take on the unperturbed electrostatic potential method},
+  journal = {The Journal of Chemical Physics}
+}
+
+@article {castep,
+    doi = {10.1524/zkri.220.5.567.65075},
+    author = {Clark, S. J. and Segall, M. D. and Pickard, C. J. and Hasnip, P. J. and Probert, M. I. J. and Refson, K. and Payne, M. C.},
+    title = {First principles methods using CASTEP},
+    journal = {Zeitschrift fuer Kristallographie},
+    volume = {220},
+    pages = {567},
+    year = {2005}
+}