Contribution Guidelines

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Getting Started

Thank you for your interest in contributing to ActinoBase! As a collaborative project, the goal of this Wiki is to collect and distribute information from Actinobacteria researchers worldwide. This page exists to give instructions on how to get started adding and editing content on the Wiki, as well as style guidelines in order to maintain the quality and consistency of the information therein.

MediaWiki pages are edited using a specific syntax, so if you'd like to write your pages in a word processor, such as Microsoft Word, you can use pandoc to convert the article to MediaWiki format for you. See the Using pandoc page for more information.

ActinoBase is still in it's development stage, so you may find pages which have not yet been brought up to the standards listed here. We are working hard to fix all of these pages as soon as we can!

Tips

To make a new page, simply add a link to it! If you would like to add a new media recipe for example, navigate to the media recipes page and click edit, type [[your media name here]]. Then press save. This will create a red link to the page (red meaning the page does not yet exist). Simply click on the red link to create the page and add your resource using the guidelines below!

Some special characters (e.g. delta, phi, lambda, degree) cannot be typed directly into ActinoBase. See the Cheat Sheet section below for a table showing the shortcuts for adding these resources, or check the XML/HTML character guide here.

To upload an image click the “Upload File” option on the toolbar. To add this image to a page use the code “[[File:your_image_filename.png |What is your image]]”, where the left component is the file name of your uploaded image, and the right side is the image title (which will appear when you hover over the image with your mouse).


General rules & guidelines

  • Please do not link to external sources without context! A hyperlink to the paper is not an experimental protocol. If you would like to contribute resources please write them out according to the guidelines below, simply hyperlinking a protocol is not helpful!
  • Within categories please keep resources listed in alphabetical order.
  • Please ensure all acronyms are defined.
  • If you don't feel your resource has an appropriate sub-category, please don't hesitate to make one.

Rules for Protocol Pages

See the links below for example pages.

Tri-parental mating

High GC PCR

Salting Out Genomic DNA Extraction Method

All protocols require the following (Note: hints & tips pages (e.g. High GC PCR) do not need to adhere to this format).

  • Title
  • List of organisms this protocols has been confirmed to work for, with citations if possible. Please also link to the relevant organisms page.
  • Brief description of the purpose of the protocol and, where necessary, the theory behind the method.
  • Materials- if specific buffers are needed please provide detailed recipes. If specific media are needed you can link to the relevant pages form the media recipes section.
  • Protocol- detailed description of each step, numbered or as bullet points.
  • Notes- any other information that is helpful or required for the protocol.
  • References- where possible refer to the original paper describing the method, or examples where the protocol has been used for actinomycetes.
  • Sign off- please sign the protocol with your name & affiliation.

Rules for Plasmid Pages

See links below for example pages.

pCRISPomyces-2

pRT802

All plasmid pages must contain the following.

  • Use- a brief description of the purpose of the vector, e.g. general purpose, or for a specific experiment (please link to this where relevant). Also, where relevant, list the organisms for which this vector has been confirmed to be useful for, and if possible provide citations for these uses. This may not be necessary for general purpose Streptomyces vectors for example.
  • Features- here please list the following where relevant
    • Phage integration site
    • Antibiotic resistance selective marker
    • E.coli Origin of replication
    • Origin of conjugative transfer
    • Any other relevant features eg. LacZ cassette for GoldenGate, or genes, tags promotors or other features relevant to the experimental use of the vector.
  • History- if possible briefly describe how the vector was made (from which backbone for example) or who by.
  • Map- Image showing the annotated plasmid map.
  • Sequence links- if possible link to an external site from which the vector sequence can be obtained, AddGene is useful for this. Please do not post the raw unannotated plasmid nucleotide sequences here. (Note: we are still in the process of finding the best solution for providing plasmid sequences, the current protocol is temporary!) .
  • References- here please provide references to the original paper describing the vector, and any relevant examples of the vectors experimental use.

Organism Pages

Coming soon!


Rules for Media Recipes

See links for example pages.

SFM

MYM

All media recipes must include the following.

  • Title- the full name of the medium, plus the acronym.

Below this please write a brief description of the medium, e.g. rich/minimal, main use.

  • Preparation- provide a detailed recipe, and Instructions for how to make the medium, especially if the medium requires and specific steps such as adjusting pH, or additives post autoclaving.
  • Uses, list the protocols and organisms this medium is used for, linking to these where relevant.
  • Notes- any other important considerations for this medium.
  • Reference- where possible provide a reference for the use of the medium.

Referencing

  • Where references are used, please provide a numbered bibliography using the Harvard format.
  • When referring to a citation in text, please do so using the bibliographical number as a superscript.


Cheat Cheet

Coming soon!