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‎README.md

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Website based on Hydra Jekyll theme `https://jekyllthemes.io/theme/hydra-jekyll-theme`
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To run locally, execute 'sudo bundle exec jekyll serve' in the main directory of the repository
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To run locally, follow the [Instructions](https://jekyllrb.com/docs/) specified in the Jekyll documentation. When you have installed all prerequisites, run:
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```sh
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gem install jekyll bundler
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```
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Enter the folder:
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```sh
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cd BAMeScience.github.io/
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```
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and install the dependencies:
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```sh
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bundle install
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```
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Then, execute:
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```sh
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bundle exect jekyll serve
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```
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to run the local server. The terminal will show the localhost where the web is deployed:
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```sh
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Configuration file: /home/<user-directory>/BAMeScience.github.io/_config.yml
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Source: /home/<user-directory>/BAMeScience.github.io
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Destination: /home/<user-directory>/BAMeScience.github.io/_site
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Incremental build: disabled. Enable with --incremental
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Generating...
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Jekyll Feed: Generating feed for posts
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done in 0.203 seconds.
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Auto-regeneration: enabled for '/home/<user-directory>/BAMeScience.github.io'
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Server address: http://127.0.0.1:4000
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Server running... press ctrl-c to stop
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```
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Click on the server address to visualize the website. You can add the option `--livereload` to serve to automatically refresh the page with each change you make to the source files:
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```sh
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bundle exect jekyll serve --livereload
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```

‎_alumni/andre.md

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---
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name: Andre Valdestilhas
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first_name_lower_case: andre
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position: Former Researcher of eScience group
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image_path: /images/team_pictures/andre.jpg
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twitter: andvaldestilhas
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blurb: Applying Semantic Web and Large Language Models to Materials Science Engineering. Google Scholar "https://scholar.google.com/citations?user=u74DYc0AAAAJ&hl"
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---
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‎_staff_members/andre.md

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‎_staff_members/angela.md

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---
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name: Angela Ariza
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first_name_lower_case: angela
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position: Researcher Data Steward
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image_path: /images/team_pictures/angela.jpg
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twitter:
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blurb: Angela is a research data steward currently working in the Data Store platform.
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---

‎_staff_members/jose.md

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---
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name: Jose M. Pizarro
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first_name_lower_case: jose
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position: Senior Data Manager
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image_path: /images/team_pictures/jose.jpg
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twitter:
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blurb: Jose is a physicist and research data management expert currently working in the Data Store platform.
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---

‎images/team_pictures/angela.jpg

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‎images/team_pictures/jose.jpg

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‎images/team_pictures/thilo.jpg

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‎publications.html

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<li>eCerto - versatile software for interlaboratory data evaluation and documentation during reference material production.
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<br /> Authors: Jan Lisec, Sebastian Recknagel, Carsten Prinz, Kristin Vogel, Matthias Koch, Roland Becker.
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Analytical and Bioanalytical Chemistry (2024). DOI: https://doi.org/10.1007/s00216-023-05099-3 <br /><br /></li>
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<li>Machine learning methods for compound annotation in non-targeted mass spectrometry—A brief overview of fingerprinting, in silico fragmentation and de novo methods.
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<br /> Authors: Francesco F. Russo, Yannek Nowatzky, Carsten Jaeger, Maria K. Parr, Phillipp Benner, Thilo Muth, Jan Lisec.
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Rapid Communications in Mass Spectrometry (2024). DOI: https://doi.org/10.1002/rcm.9876 <br /><br /></li>
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<li>Robust Entropy Search for Safe Efficient Bayesian Optimization.
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<br /> Authors: Dorina Weichert, Alexander Kister, Patrick Link, Sebastian Houben, Gunar Ernis.
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arXiv preprint arXiv:2405.19059 <br /><br /></li>

‎team/andre.html

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---
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title: Andre Valdestilhas
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description: Researcher
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description: Former Researcher
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---
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<img src="/images/team_pictures/andre.jpg" alt="Profile Picture Andre" class="center">
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</div>
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<div class="personal_description">
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Areas: Semantic Web applyied to Material Sciences Engineering.
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Bachelor: 1999-2003 (Computer Science). Masters: 2006-2009 (Interactive Television). PhD 2014-2020 (Semantic
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Web). With experience as a scholar and in industry. A motivated and active researcher who has helped organize various scientific events. These events include conferences and workshops, where he have taken on roles such as chair, program committee member, and reviewer, such as ICWI (https://www.internet-conf.org/), ESWC, ISWC, ICSC (IEEE International Conference on Semantic Computing) (https:
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//www.ieee-icsc.org/), CSCUBS (http://cscubs.cs.uni-bonn.de/), INNOV (https://www.iaria.org/conferences/INNOV.html), FutureTech (http://www.futuretech-conference.org/), QuWeDa 2019-2023 (https://sites.google.com/site/quweda2019/home), The Semantic Web Journal (http://www.semantic-web-journal.net/), BIS (Business Information Systems conference) (https://bisconf.org/), SeMats workshop (https://semats.aksw.org/).
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Hobbies: Skateboard, guitar, drinking beer(Rock n roll, yhuuu!)
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Computer science researcher with 20+ years of experience. Skilled in applying semantic web technologies and large language models to materials science research, social sciences, and the humanities. Proven track record in research leadership and publication. Extensive experience in conference organization and participation (chair, program committee, reviewer) at top venues like ICWI, ESWC, ISWC, and The Semantic Web Journal. Led the organization of the scientific workshop SeMats <a href="https://semats.aksw.org/" style="text-decoration:none">
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<span style="font-size:11pt"><span style="font-family:Arial,sans-serif"><span style="color:#1155cc"><u>https://semats.aksw.org/</u>
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</span></span></span></a>. My key competencies and skills are teaching and research.
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</div>
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</section>
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<p><span style="font-size:11pt"><span style="font-family:Arial,sans-serif"><span style="color:#000000">Social media:</span></span></span></p>
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<p><span style="font-size:13pt"><span style="font-family:Arial,sans-serif"><span style="color:#000000">Social media:</span></span></span></p>
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<ul>
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<li style="list-style-type:disc"><span style="font-size:11pt"><span style="font-family:Arial,sans-serif"><span style="color:#000000">Twitter/X: https://twitter.com/andvaldestilhas</span></span></span></a></li>
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<li style="list-style-type:disc"><span style="font-size:11pt"><span style="font-family:Arial,sans-serif"><span style="color:#000000">Linkedin: https://www.linkedin.com/in/dr-andre-valdestilhas-99196521/<</span></span></span></li>
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<li style="list-style-type:disc"><span style="font-size:11pt"><span style="font-family:Arial,sans-serif"><span style="color:#000000">Twitter/X: <a href="https://twitter.com/andvaldestilhas" target="_blank">andvaldestilhas</a></span></span></span></li>
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<li style="list-style-type:disc"><span style="font-size:11pt"><span style="font-family:Arial,sans-serif"><span style="color:#000000">Linkedin: <a href="https://www.linkedin.com/in/dr-andre-valdestilhas-99196521/" target="_blank">dr-andre-valdestilhas-99196521</a></span></span></span>
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<li style="list-style-type:disc"><span style="font-size:11pt"><span style="font-family:Arial,sans-serif"><span style="color:#000000">ORCID: <a href="https://orcid.org/0000-0002-0079-2533" target="_blank">0000-0002-0079-2533</a></span></span></span>
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<li style="list-style-type:disc"><span style="font-size:11pt"><span style="font-family:Arial,sans-serif"><span style="color:#000000">Google Scholar: <a href="https://scholar.google.com/citations?hl=en&amp;user=u74DYc0AAAAJ" target="_blank">user=u74DYc0AAAAJ</a></span></span></span>
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</li>
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</ul>
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<section>
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<p><span style="font-size:11pt"><span style="font-family:Arial,sans-serif"><span style="color:#000000">2024</span></span></span></p>
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<p><span style="font-size:13pt"><span style="font-family:Arial,sans-serif"><span style="color:#000000">2024</span></span></span></p>
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<p>&nbsp;</p>
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<p><span style="font-size:11pt"><span style="font-family:Arial,sans-serif"><span style="color:#000000">Conferences and workoshop organization:</span></span></span></p>
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<p><span style="font-size:13pt"><span style="font-family:Arial,sans-serif"><span style="color:#000000">Conferences and workoshop organization:</span></span></span></p>
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<ul>
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<li style="list-style-type:disc"><span style="font-size:11pt">
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</span></span></span></a>colocated at SEMANTICS 2024 conference (https://2024-eu.semantics.cc/)</li>
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</ul>
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<p>&nbsp;</p>
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<p><span style="font-size:11pt"><span style="font-family:Arial,sans-serif"><span style="color:#000000">2023</span></span></span></p>
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<p><span style="font-size:13pt"><span style="font-family:Arial,sans-serif"><span style="color:#000000">2023</span></span></span></p>
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<p>&nbsp;</p>
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<p><span style="font-size:11pt"><span style="font-family:Arial,sans-serif"><span style="color:#000000">Publications (Full papers):</span></span></span></p>
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<p><span style="font-size:13pt"><span style="font-family:Arial,sans-serif"><span style="color:#000000">Publications (Full papers):</span></span></span></p>
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<ul>
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<li style="list-style-type:disc"><span style="font-size:11pt"><span style="font-family:Arial,sans-serif"><span style="color:#000000">Valdestilhas, Andre, Bernd Bayerlein, Benjamin Moreno Torres, Ghezal Ahmad Jan Zia, and Thilo Muth. &quot;The Intersection Between Semantic Web and Materials Science.&quot; Advanced Intelligent Systems (2023). DOI: </span></span></span><a href="https://doi.org/10.1002/aisy.202300051" style="text-decoration:none"><span style="font-size:11pt"><span style="font-family:Arial,sans-serif"><span style="color:#1155cc"><u>https://doi.org/10.1002/aisy.202300051</u></span></span></span></a></li>
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<li style="list-style-type:disc"><span style="font-size:11pt"><span style="font-family:Arial,sans-serif"><span style="color:#000000">A. Valdestilhas, T. Hanke, S. Javadimasoudian, G. Zia, H. Feleemberg, T. Muth, NaturalMSEQueries&mdash;A Natural Way to Query Materials Science Engineering Data Experiments, 2023, </span></span></span><a href="https://doi.org/10.5281/zenodo.7744532" style="text-decoration:none"><span style="font-size:11pt"><span style="font-family:Arial,sans-serif"><span style="color:#1155cc"><u>https://doi.org/10.5281/zenodo.7744532</u></span></span></span></a><span style="font-size:11pt"><span style="font-family:Arial,sans-serif"><span style="color:#000000">.In Proceeding ICWI 2023 (https://www.iadisportal.org/ac-icwi-2023-proceedings).</span></span></span></li>
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</ul>
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<p><span style="font-size:11pt"><span style="font-family:Arial,sans-serif"><span style="color:#000000">Posters in conferences:</span></span></span></p>
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<p><span style="font-size:13pt"><span style="font-family:Arial,sans-serif"><span style="color:#000000">Posters in conferences:</span></span></span></p>
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<li style="list-style-type:disc"><span style="font-size:11pt"><span style="font-family:Arial,sans-serif"><span style="color:#000000">VALDESTILHAS, A.; Todor, A; Hanke, T; Muth, T. MatPortal.org - The Ontology Repository for Materials Science. (NFDI Matwerk 2023) https://nfdi-matwerk.de/nfdi/2023/</span></span></span></li>

‎team/angela.html

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---
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title: Angela Ariza
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description: Researcher Data Steward
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---
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<div class="team_members">
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<section>
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<div class="profile_picture">
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<img src="/images/team_pictures/angela.jpg" alt="Profile Picture Angela" class="center">
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</div>
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<div class="personal_description">
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Angela A has been working as a data steward at the eScience Group since 2022. She provides training and support for onboarding BAM departments to BAM's central research data management system based on the open source
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<a href="https://openbis.ch/">openBIS</a> openBIS-software.
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Angela previously worked as a researcher at Charité as part of the Berlin University Alliance project to identify researchers' needs for managing research data in line with RDM best practices. The project aimed to develop collaborative RDM services for the four Berlin universities.
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Angela holds a PhD in Natural Sciences with a focus on stem cells and tissue engineering from the Technical University of Berlin. She conducted her postdoctoral research in the field of biomedical sciences with focus on cell and tissue imaging in the Department of Experimental Radiology at Charité.
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</div>
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</section>
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<section>
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<div class="socials">
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<a target="_blank" href="https://orcid.org/0000-0002-1005-5780">ORCID</a>
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</div>
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</section>
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<section>
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<ul class="publications">
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<p>Publications:</p>
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<li>El-Athman, R., Rädler, J., Löhmann, O., Ariza de Schellenberger, A., & Muth, T. (2023)
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The BAM Data Store: Piloting an openBIS-Based Research Data Infrastructure for Materials Science and Engineering.
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1st Conference on Research Data Infrastructure (CoRDI) - Connecting Communities. (CoRDI-NFDI), Karlsruhe (Germany) . Zenodo. https://doi.org/10.5281/zenodo.8359945</li>
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<li>Ariza de Schellenberger, A., Bobrov, E., Helbig, K., Jäckel, D., Kuberek, M., Orozco Prado, L.-S., Schlagberger, E. M., Söring, S., & Steinke, B. (2022)
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Bestands- und Bedarfserhebung zum Forschungsdatenmanagement an den BUA-Einrichtungen (Version 1).Zenodo. https://doi.org/10.5281/zenodo.7060446</li>
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<li>Jan Taubitz, Evgeny Bobrov, & Angela Ariza de Schellenberger. (2022)
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Auswertung der Bedarfserhebung zum Forschungsdatenmanagement an der Charité 2021/22 (Analysis of the survey on research data management at Charité 2021/22) (v1.3.0)
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Zenodo. https://doi.org/10.5281/zenodo.7385548 </li>
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<li>Angela Ariza de Schellenberger,Harald Kratz,Tracy D Farr,Norbert Löwa,alf Hauptmann,Susanne Wagner,Matthias Taupitz,Jörg Schnorr,Eyk A Schellenberger. (2016)
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Labeling of mesenchymal stem cells for MRI with single-cell sensitivity.
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International Journal of Nanomedicine. DOI: 10.2147/ijn.s101141
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</ul>
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</section>
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</div>

‎team/jose.html

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---
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title: Jose M. Pizarro
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description: Senior Data Manager
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---
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<div class="team_members">
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<section>
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<div class="profile_picture">
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<img src="/images/team_pictures/jose.jpg" alt="Profile Picture Jose" class="center">
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</div>
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<div class="personal_description">
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Jose M. Pizarro (a.k.a. Chema) is working as a permanent researcher in Research Data Management at the eScience
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group since November 2024. He is involved in the BAM Data Store project and on simulating electronic properties of
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materials. His work is focused on software development for the BAM Data Store, data modeling and ontologies
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development, and automation of simulation workflows.
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Chema previously completed his Ph.D. in Physics at the Instituto de Ciencia de Materiales de Madrid (ICMM). He
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worked as a Postdoctoral Research Associate at the University of Bremen and the Max Planck Institute for the
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Structures and Dynamics of Matter (MPSD) in Hamburg, and as a Software Developer and Data Management expert at the consortium
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FAIRmat, in the Humboldt University of Berlin.
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</div>
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</section>
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<section>
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<div class="socials">
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See personal <a target="_blank" href="https://josepizarro3.github.io/">website</a> for more information.
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</div>
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</section>
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</div>

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