ORCA paper

[tmozgach]

Title:? Format: Application note (2 pages) Deadline:? Journals:

• [x] Bioinformatics provides a forum for the exchange of information in the fields of computational molecular biology and post-genome bioinformatics, with emphasis on the documentation of new algorithms and databases that allows the progress of bioinformatics and biomedical research in a significant manner. (https://academic.oup.com/bioinformatics)

• [ ] Bioinformatics and Biology Insights The journal welcomes all submissions in the field of bioinformatics and also submissions dealing with the relationship between bioinformatics and the broader field of biology. Submissions of original research, reviews, tutorials, rapid communications, expert commentaries, letters, application notes, and point–counter-point articles are welcomed for peer review. (http://insights.sagepub.com/journal.php?pa=aims_and_scope&journal_id=39)

• [ ] BMC Bioinformatics is an open access, peer-reviewed journal that considers articles on all aspects of the development, testing and novel application of computational and statistical methods for the modeling and analysis of all kinds of biological data, as well as other areas of computational biology. (https://bmcbioinformatics.biomedcentral.com/about)

• [ ] OUP Database is platform for the presentation of novel ideas in database research surrounding biological information, and aims to help strengthen the bridge between database developers, curators, and users. (https://academic.oup.com/database/pages/About)

• [ ] Briefings in Bioinformatics The journal publishes reviews for the users of databases and analytical tools of contemporary genetics, molecular and systems biology and is unique in providing practical help and guidance to the non-specialist in computerized methodology. (https://academic.oup.com/bib/pages/About)

• [ ] Computational and Structural Biotechnology Journal The journal places a strong emphasis on functional and mechanistic understanding of how molecular components in a biological process work together through the application of computational methods. The journal welcomes the submission of manuscripts that meet the general criteria of significance and scientific excellence, and enables the rapid publication of papers under the following categories: Research articles Review articles Mini Reviews Highlights Communications Software/Web server articles (https://www.journals.elsevier.com/computational-and-structural-biotechnology-journal)

• [ ] EMBNET.JOURNAL The main focus of EMBnet.journal is on the latest developments in bioinformatics research, in tools and resources, in training and education, and in standards and best practice. (https://www.embnet.org/wp/)

• [x] GigaScience As an open access and open-data journal, we publish ALL research objects (data, software tools and workflows) from 'big data' studies across the entire spectrum of life and biomedical sciences. (https://academic.oup.com/gigascience)

• [ ] eLife publishes important research in all areas of the life and biomedical sciences. (https://elifesciences.org/about) Structure:

[sjackman]

I believe OUP Database is the journal that Steve suggested: https://academic.oup.com/database

[tmozgach]

@sjackman I have done a small summary of Bioinformatics journals and bolted the main ideas, feel free to add another journals and review my list!

[sjackman]

For the literature review, you can compare ORCA to BioContainers http://biocontainers.pro and possibly Bioboxes http://bioboxes.org

The Linuxbrew package manager can be compared to Bioconda https://bioconda.github.io The Spack package manager also has a paper: https://computation.llnl.gov/projects/spack-hpc-package-manager https://doi.org/10.1145/2807591.2807623

[sjackman]

Two more possible journals: GigaScience and eLife

[tmozgach]

The paper about biocontaines can be good example and we can try to target the same journal:

https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btx192

[tmozgach]

Bioboxes: https://gigascience.biomedcentral.com/articles/10.1186/s13742-015-0087-0

[sjackman]

I've create a GitHub repo for the paper https://github.com/sjackman/orca-paper

[tmozgach]

The target journals: Bioinformatics, GigaScience (Plan B =) )

[tmozgach]

Dugong: https://www.ncbi.nlm.nih.gov/pubmed/28968637

[tmozgach]

Main workplace is here: https://github.com/sjackman/orca-paper