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Author Contributions {.page_break_before}

SL conceptualised and developed the platform and wrote the manuscript. SF integrated BioChatter continuous integration pipelines and developed both front-end and back-end components for the BioChatter Next server. The BioChatter consortium members contributed to the development of the platform and provided feedback on the manuscript. AM implemented the local deployment functionality. CW architected the BioChatter Next server infrastructure. JB provided guidance and supervision as well as hardware resources for local LLM use and contributed to performance benchmarking. NK implemented benchmarking procedures. QM oversaw the development and deployment of the BioChatter Next server environment. JSR supervised the project, revised the manuscript, and acquired funding. All authors read and approved the final manuscript.

Acknowledgements

We thank Hanna Schumacher, Daniel Dimitrov, Pau Badia i Mompel, and Aurelien Dugourd for feedback on the original draft of the manuscript and the software.

This work was supported by funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 965193 (JSR), award U54-AG075931 (QM) from the National Institutes of Health, award NSF1945971 (QM) from the National Science Foundation, and the Pelotonia Institute of Immuno-Oncology.

Disclaimer

This project is funded by the European Union under grant agreement No. 101057619. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or European Health and Digital Executive Agency (HADEA). Neither the European Union nor the granting authority can be held responsible for them. This work was also partly supported by the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract No. 22.00115.

Conflict of Interest

JSR reports funding from GSK, Pfizer and Sanofi and fees/honoraria from Travere Therapeutics, Stadapharm, Pfizer, Grunenthal, Owkin, and Astex Pharmaceuticals.

References {.page_break_before}

The BioChatter Consortium

The BioChatter Consortium is a community of researchers and developers who are interested in the application of LLMs to biomedical research. We list here alphabetically all members of the consortium who have contributed to the development of the BioChatter framework.

  • Adrián G. Díaz (Interuniversity Institute of Bioinformatics in Brussels, Brussels, Belgium and Structural Biology Brussels, Vrije Universiteit Brussels, Brussels, Belgium)
  • Andreas Maier (Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany)
  • Aurelien Dugourd (Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany)
  • Cankun Wang (Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA)
  • Emma Verkinderen (Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050, Brussels, Belgium)
  • Fernando M. Delgado-Chaves (Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany)
  • Jan Baumbach (Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany and Computational Biomedicine Lab, Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark)
  • Julio Saez-Rodriguez (Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany)
  • Megan McNutt (Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA)
  • Nils Krehl (Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany)
  • Qin Ma (Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA)
  • Sebastian Beier (Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Bioeconomy Science Center (BioSC), CEPLAS, Forschungszentrum Jülich, Jülich, Germany)
  • Sebastian Lobentanzer (Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute for Computational Biomedicine, Heidelberg, Germany)
  • Shaohong Feng (Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA)
  • Trang T. Le (Bristol Myers Squibb, 250 Water St, Cambridge, MA 02141, USA)
  • Xiao-Ran Zhou (Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Bioeconomy Science Center (BioSC), CEPLAS, Forschungszentrum Jülich, Jülich, Germany)
  • Yuyao Song (European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, United Kingdom)