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Author instructions

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Pjotr Prins edited this page Nov 21, 2019 · 3 revisions

For the biohackathons we are initiating a special arxiv pre-publication server. These mini-publications allow you to expose your work as a citeable document (a DOI will be included). Please create the document as markdown and add a link to the project pages. Also add a link to your slide.

The outline of the group publication is discussed below:

In the pre-print process we should emphasize the structure of a (pre-publishable) subdocument. Outline:

Project title

Authors with ORCIDs(!)

(the first author is the point person for the mini-publication, unless explicitly specified)

  1. State the problem you worked on
  2. Give the state-of-the art/plan
  3. Describe what you have done/results starting with The working group created...
  4. Write a conclusion
  5. Write up any future work
  6. Add references
  7. Add URLs to any source code, software, notebooks, documentation and/or data relevant to this publication with a short description.

The last one is very important because it allows us to create a meta-bundle of your resource. The full publication is the mini-publication plus everything that is included as resource objects (ROs).

We suggest to use either github markdown (wiki or a README.md) or the https://osf.io/ wiki pages which you can create when you open an account with ORCID. HackMD is another option. Make sure we can find this information by adding a group page on the wiki of this biohackathon.

In addition provide a figure with caption (if applicable) and Also provide a URL to your Jupyter notebook/github repo and data (as research objects)

The general idea is that we will compile a metadocument as the biohackathon 2019 report. When every project sticks to this layout the reader knows what to expect when reading about every project. This is about the reader experience rather than the author experience! So please stick with this 'flow'.

Example of a very short publication:

Title: Making the Sequence Read Archive public and searchable

(State the problem) Information from next-generation sequencing experiments is separately archived to different databases including: the Sequence Read Archive (SRA) (Leinonen et al., 2010), the National Center for Biotechnology Information’s (NCBI) BioProject (Barrett et al., 2011), and BioSample (Courtot et al., 2018). (State of the art/plan) The working group aimed to make information in the SRA public and searchable (Figure 7). (Work executed) The following tasks were accomplished during the BH17: 1) customized the system to follow DNA Databank of Japan (DDBJ) (Stoesser, 2004) requests; 2) defined specifications for a brand new Database Center for Life Science (DBCLS) SRA (Leinonen et al., 2010)) Web user interface; 3) converted BioProject and BioSample data to RDF; and 4) developed a prototype method for searching reads by expression pattern. (Future work) In the future, the working group will integrate the SRA with BioProject and BioSample metadata as well as develop a Web user interface.

(figure and references)

Make sure references are added in the format:

Authors (surname, letters) (year). Title. Journal ref. DOI.

    Adachi, T., Kawamura, K., Furusawa, Y., Nishizaki, Y., Imanishi, N., Umehara,
    S., et al. (2017). Japan’s 827 initiative on rare and undiagnosed diseases
    (IRUD): towards an end to the diagnostic odyssey. Eur. J. 828 Hum. Genet. 25,
    1025

Finally add links to all resources you used for this publication.

Example of a more elaborate publication

Project Reporting Example

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