Merge pull request #5907 from BiodataAnalysisGroup/dome-training

Dome training material for AI school.

Author: anuprulez

CONTRIBUTORS.yaml

@@ -3079,3 +3079,14 @@ rmassei:
     joined: 2024-11
     affiliations:
       - nfdi4bioimage
+
+sfragkoul:
+    name: Stella Fragkouli
+    email: [email protected]
+    twitter: scfragkoul
+    linkedin: sfragkoul
+    orcid: 0000-0003-4067-7123
+    joined: 2025-03
+    elixir_node: gr
+    affiliations:
+      - elixir-europe

topics/statistics/tutorials/dome/images/ML_Biology.png

@@ -6,7 +6,8 @@
 contributions:
   authorship:
   - fpsom
+  - sfragkoul 
 tags:
   - elixir
   - ai-ml
----
+---

topics/statistics/tutorials/dome/slides.html

@@ -0,0 +1,98 @@
+@article{gruning2018practical,
+  title={Practical computational reproducibility in the life sciences},
+  author={Gr{\"u}ning, Bj{\"o}rn and Chilton, John and K{\"o}ster, Johannes and Dale, Ryan and Soranzo, Nicola and Van Den Beek, Marius and Goecks, Jeremy and Backofen, Rolf and Nekrutenko, Anton and Taylor, James},
+  journal={Cell systems},
+  volume={6},
+  number={6},
+  pages={631--635},
+  year={2018},
+  publisher={Elsevier},
+  doi={10.1016/j.cels.2018.03.014},
+}
+
+@article{jones2019setting,
+  title={Setting the standards for machine learning in biology},
+  author={Jones, David T},
+  journal={Nature Reviews Molecular Cell Biology},
+  volume={20},
+  number={11},
+  pages={659--660},
+  year={2019},
+  publisher={Nature Publishing Group UK London},
+  doi={10.1038/s41580-019-0176-5},
+}
+
+@article{necci2020mobidb,
+  title={MobiDB-lite 3.0: fast consensus annotation of intrinsic disorder flavors in proteins},
+  author={Necci, Marco and Piovesan, Damiano and Clementel, Damiano and Doszt{\'a}nyi, Zsuzsanna and Tosatto, Silvio CE},
+  journal={Bioinformatics},
+  volume={36},
+  number={22-23},
+  pages={5533--5534},
+  year={2020},
+  publisher={Oxford University Press},
+  doi={10.1093/bioinformatics/btaa1045},
+}
+
+
+@article{sandve2013ten,
+  title={Ten simple rules for reproducible computational research},
+  author={Sandve, Geir Kjetil and Nekrutenko, Anton and Taylor, James and Hovig, Eivind},
+  journal={PLoS computational biology},
+  volume={9},
+  number={10},
+  pages={e1003285},
+  year={2013},
+  publisher={Public Library of Science San Francisco, USA},
+  doi={10.1371/journal.pcbi.1003285},
+}
+
+@article{walsh2015comprehensive,
+  title={Comprehensive large-scale assessment of intrinsic protein disorder},
+  author={Walsh, Ian and Giollo, Manuel and Di Domenico, Tom{\'a}s and Ferrari, Carlo and Zimmermann, Olav and Tosatto, Silvio CE},
+  journal={Bioinformatics},
+  volume={31},
+  number={2},
+  pages={201--208},
+  year={2015},
+  publisher={Oxford University Press},
+  doi={10.1093/bioinformatics/btu625},
+}
+
+
+@article{walsh2016correct,
+  title={Correct machine learning on protein sequences: a peer-reviewing perspective},
+  author={Walsh, Ian and Pollastri, Gianluca and Tosatto, Silvio CE},
+  journal={Briefings in bioinformatics},
+  volume={17},
+  number={5},
+  pages={831--840},
+  year={2016},
+  publisher={Oxford University Press},
+  doi={10.1093/bib/bbv082},
+}
+
+
+@article{walsh2021dome,
+  title={DOME: recommendations for supervised machine learning validation in biology},
+  author={Walsh, Ian and Fishman, Dmytro and Garcia-Gasulla, Dario and Titma, Tiina and Pollastri, Gianluca and Harrow, Jennifer and Psomopoulos, Fotis E and Tosatto, Silvio CE},
+  journal={Nature methods},
+  volume={18},
+  number={10},
+  pages={1122--1127},
+  year={2021},
+  publisher={Nature Publishing Group US New York},
+  doi={10.1038/s41592-021-01205-4},
+}
+
+@article{wilkinson2016fair,
+  title={The FAIR Guiding Principles for scientific data management and stewardship},
+  author={Wilkinson, Mark D and Dumontier, Michel and Aalbersberg, IJsbrand Jan and Appleton, Gabrielle and Axton, Myles and Baak, Arie and Blomberg, Niklas and Boiten, Jan-Willem and da Silva Santos, Luiz Bonino and Bourne, Philip E and others},
+  journal={Scientific data},
+  volume={3},
+  number={1},
+  pages={1--9},
+  year={2016},
+  publisher={Nature Publishing Group},
+  doi={10.1038/sdata.2016.18},
+}