Destination Journal

[FReina]

Hi,

Turns out "Methods" by Elsevier is invite-only. I do not know if CE knows if we can get invited to an issue, I will ask further. Other Journals we can consider, in order of my preference:

• Bioinformatics (4.531): the author guideline for the scope Data and Text Mining says:

  "Data and Text Mining This category includes: New methods and tools for extracting biological information from text, databases and other sources of information. Description of tools to organize, distribute and represent this information. New methods for inferring and predicting biological features based on the extracted information. The submission of databases and repositories of annotated text, computational tools and general methodology for the work in this area are encouraged, provided that they have been previously tested. The journal requires that methods, systems and data to be made public. Strong emphasis should be placed on the biological applicability of the methods and the application to realistic biological scenarios. The main interest of the journal is the application to problems in molecular biology, but we also encourage submissions related with the relation between molecular and other type of data such as clinical, epidemiological, evolutionary, genomics, and others. Combination of information extraction technologies from heterogeneous sources and the combination with various computational approaches is also encouraged. The journal is not primarily interested in publishing analysis related with the sociological aspects of publications. The use of standard data sets for the evaluation of the methods is strongly advised, as well as the comparison with previous methods using common data sets."

and I think we fit in here pretty well.

• Journal of Experimental Biology (3.017) as a "Methods & Techniques" paper:

"Methods & Techniques are short, peer-reviewed articles reporting innovative methodological advances or significant modifications to recognized methods of data collection and analysis. The total length of the article (including the main text and figure legends, but not the title page, abstract, materials and methods section or reference list) should not exceed 2500 words, with a 150-word abstract and a maximum of 3 display items (figures/tables). Where possible, the use of the method should be demonstrated by applying it to real physiological data, but it is not necessary to apply the method to test a hypothesis. Methods should be described in enough detail to allow others to replicate and verify the protocol and must show a significant improvement on previous techniques. All methodology should be given within the Materials and methods section, although additional figures, tables and movies may be published online as supplementary information at the discretion of the editor and reviewers (there is a strict limit of 50 Mb per article). Mathematical calculations should be placed in an Appendix if they are likely to interrupt the flow of the manuscript. Manuscripts should be divided into the following sections, in this order:

Title page
Abstract (max. 150 words)
Introduction
Materials and methods
Results and discussion
Appendix (if applicable)
Acknowledgements
Competing interests
Author contributions
Funding
References
Figure legends
Tables"

I will discover about "Methods" on Thursday, more or less, and let you know more

[MariiaVision]

• Bioinformatics :the scope Data and Text Mining - accepts computation tools, I would say it will be more realistically to target.
• Journal of Experimental Biology as a "Methods & Techniques" paper - we are not introducing new techniques or methods, so I wouldn't target this one.

[FReina]

We asked Methods if they are interested and could invite us. If so, we go for it, otherwise, Bioinformatics.

[FReina]

* Bioinformatics :the scope Data and Text Mining - accepts computation tools, I would say it will be more realistically to target.

* Journal of Experimental Biology as a "Methods & Techniques" paper - we are not introducing new techniques or methods, so I wouldn't target this one.

In general however I agree with this, I think it's the best option. Here is a link to one of their papers: https://academic.oup.com/bioinformatics/article/36/6/1978/5625619

The "article" itself is little more than an introduction and description. Most of it is actually in the supplementary data, which is written more freely.

[FReina]

This is how we agreed to proceed:

• we (but mainly I) will make a brief piece in which we describe the problem, give a motivation of the project, describe briefly what it does, and concludes that it is a good piece of software that can help mainly with data analysis of single particle tracks;

• we, according to the contribution we gave to the project, will describe how it works and how it does it. I also think giving some example movies and csv with trajectories that can be used for testing will go a long way.

Personally, we should model it to https://academic.oup.com/bioinformatics/article/32/6/958/1744608 and https://academic.oup.com/bioinformatics/article/32/6/952/1744407#supplementary-data. Dominic's paper has got no supplementary, and the other one as an extensive description, so we can write as much as we please.

Initial release will be on Biorxiv, and submitted to Bioinformatics.