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Improving Reproducibility and Reusability in the Journal of Cheminformatics

Journal of Cheminformatics is piloting the inclusion of an additional software reproducibility and reusability review with its new submissions. Any author whose submission has an associated code repository is free to participate in this pilot, but are encouraged to read the editorial by Hoyt et al. before submitting.

Papers submitted to the pilot will undergo enhanced peer review featuring a reproducibility and reusability review that examines the following seven questions:

  1. Does the repository contain a LICENSE file in its root?
  2. Does the repository contain a README file in its root?
  3. Does the repository contain an associated public issue tracker?
  4. Has the repository been externally archived on Zenodo, FigShare, or equivalent that is referenced in the README?
  5. Does the README contain installation documentation?
  6. Is the code from the repository installable in a straight-forward manner?
  7. Does the code in the conform to an external linter (e.g., black for Python)?

These correspond to important details that are complementary to other considerations of reproducibility, but often overlooked. Throughout the pilot, the editors and reviewers will try to support authors in addressing each of these points during revision.

Authors should follow the Submission Guidelines for the journal as normal and select "Improving reproducibility and reusability in the Journal of Cheminformatics" from the Collection dropdown menu during the submission process.

Guest Editor
Charles Tapley Hoyt, Harvard Medical School, USA


  1. Natural products are molecules that fulfil a range of important ecological functions. Many natural products have been exploited for pharmaceutical and agricultural applications. In contrast to many other speci...

    Authors: Barbara R. Terlouw, Friederike Biermann, Sophie P. J. M. Vromans, Elham Zamani, Eric J. N. Helfrich and Marnix H. Medema
    Citation: Journal of Cheminformatics 2024 16:106
    Content type: Software Published on:

  2. One challenge that current de novo drug design models face is a disparity between the user’s expectations and the actual output of the model in practical applications. Tailoring models to better align with che...

    Authors: Janosch Menke, Yasmine Nahal, Esben Jannik Bjerrum, Mikhail Kabeshov, Samuel Kaski and Ola Engkvist
    Citation: Journal of Cheminformatics 2024 16:100
    Content type: Software Published on:

  4. Machine learning is becoming a preferred method for the virtual screening of organic materials due to its cost-effectiveness over traditional computationally demanding techniques. However, the scarcity of labe...

    Authors: Chengwei Zhang, Yushuang Zhai, Ziyang Gong, Hongliang Duan, Yuan-Bin She, Yun-Fang Yang and An Su
    Citation: Journal of Cheminformatics 2024 16:89
    Content type: Research Published on:

  6. Reaction databases are a key resource for a wide variety of applications in computational chemistry and biochemistry, including Computer-aided Synthesis Planning (CASP) and the large-scale analysis of metaboli...

    Authors: Tieu-Long Phan, Klaus Weinbauer, Thomas Gärtner, Daniel Merkle, Jakob L. Andersen, Rolf Fagerberg and Peter F. Stadler
    Citation: Journal of Cheminformatics 2024 16:82
    Content type: Methodology Published on:

  7. Previous deep learning methods for predicting protein binding pockets mainly employed 3D convolution, yet an abundance of convolution operations may lead the model to excessively prioritize local information, ...

    Authors: Ruifeng Zhou, Jing Fan, Sishu Li, Wenjie Zeng, Yilun Chen, Xiaoshan Zheng, Hongyang Chen and Jun Liao
    Citation: Journal of Cheminformatics 2024 16:79
    Content type: Research Published on:

  8. SMILES-based generative models are amongst the most robust and successful recent methods used to augment drug design. They are typically used for complete de novo generation, however, scaffold decoration and f...

    Authors: Morgan Thomas, Mazen Ahmad, Gary Tresadern and Gianni de Fabritiis
    Citation: Journal of Cheminformatics 2024 16:77
    Content type: Research Published on:

  10. In recent years, cheminformatics has experienced significant advancements through the development of new open-source software tools based on various cheminformatics programming toolkits. However, adopting thes...

    Authors: Venkata Chandrasekhar, Nisha Sharma, Jonas Schaub, Christoph Steinbeck and Kohulan Rajan
    Citation: Journal of Cheminformatics 2023 15:98
    Content type: Software Published on: