User:Cellular Biochemistry II/Tutorial

This page should coordinate the efforts of writing good Wikipedia articles for the course "Cellular Biochemistry". Please note that Wikipedia uses a Markup Language to create content, so unlike in Microsoft Word or OpenOffice.org Writer you dont get what you see but what you mean. It is similar to HTML or LaTeX, some commands you know from there you will be able to use here again. If you are not familiar with Wikipedia markup language, you can always consult the Wikipedia:Cheatsheet.

If you want to get started, just copy and paste the #Sample Article from this tutorial.

Tutorial Summary

The first thing you should do is read this tutorial carefully, just click on "show" and be sure to understand these points.

If you don't want to read it all, here is a short summary: Get an account by clicking on Log in / create account. If you want to experiment, the right place is the Wikipedia:Sandbox. Check what information Wikipedia already provides on your topic using a command like "mitochondrion inurl:en.wikipedia.org" in Google. Then start writing your article like described below in the section "Sample Article", write it according to Wikipedias guidelines and the ones given to you by the course instructor. Do NOT use your own made up theories or data, use only material that is already published, preferentially in a peer reviewed journal. Indicate your sources by referencing, see Wikipedia:Citing sources. Use internal and external links to make your article more understandable, the internal "wiki links" are one of the strongest advantages of Wikipedia, use them when appropriate but do not link every word ;-). Put external links at the end to the "external links" section.

Start your article with the template provided here. Make it easy and understandable for the layperson. Try to think of the people that read the article, think about what you would want to know or what might be interesting. Write encyclopedic style, do not write Protein A is the best, I prefer it over protein B but rather write Protein A is important in cell cycle control and it is phosphorylated at Tyr43 by protein B.

If you want to learn how to make nice pictures using PyMol, use this tutorial.

Links and Tools

In case you need further help, you probably want to check these links to answer questions which might arise while you work on your article

These two tools might come in handy editing the article or creating correctly formatted references:

The "wikEd" Editor or any other editor from Wikipedia:Text_editor_support (I personally prefer the It's All Text! Firefox plugin together with vim)
Template Filler

Pictures

The most important issue for images is their copyright status. Images in the public domain, or released under one of the free licenses compatible with Wikipedia, can be uploaded at will. In other cases, the uploader should own the copyright and be willing to release the image. The various issues surrounding image copyright on Wikipedia are discussed here and at the linked articles. But you cannot just upload an image from a journal like Nature since these journals do not publish their material under a free license. So there are several options you have:

Use a free image, either from a journal like PLoS or from a database like the PDB -- in the latter case use the {{PD-release}}) template to indicate the release into the public domain.
Create your own image using GIMP or Adobe Illustrator; or just draw it and then scan it. Then select an appropriate license, if you are not sure which one to choose, you are on the safe side with {{PD-self}}).
Ask the owners of an image to release it under the Creative Commons Licence (ATTENTION the owner is usually NOT the author of the paper but the journal!). This is usually the hardest way to get a picture into an article. You must provide the email as proof that the owner gave permission to publish the work under Creative Commons. If you want to do that, you better contact Hannes.

Once you have your image, use the Cellular Biochemistry II account (or your own) to go to Wikimedia Commons to upload the image. You will have to use an account to upload the image, you cannot do so anonymously. Once you clicked on "upload image", you get to a page where you can either select It is entirely my own work or It is from somewhere else, you most likely will not need any of the other options. There are a couple of fields you have to fill out, most importantly the Description and the License field. Then you can click on upload and you are done.

License tags

License tags like {{PD-release}}) or {{PD-self}}) should be included in the text of the site where the image resides. For an example, see here: http://en.wikipedia.org/wiki/File:Atg1_interaction_partners.jpg -- if you click on edit, you see how the license tag is added correctly to the image.

Inlcude in your article

Then you can use it in your article:

To include an image in an article, add the image file name between double square brackets, preceded by the word “Image:”, e.g., “[[Image:Proteasome.jpg]]". The image can be aligned with the right or left margin using those words as arguments, as in “[[Image:Proteasome.jpg|right]]"; right alignment is the default. Wikipedia's image policy strongly encourages using the 'thumbnail' size for most images, as in “[[Image:Proteasome.jpg|right|thumb]]", but an image that requires larger display, such as a map or diagram, can be scaled by specifying a pixel size, as in “[[Image:Proteasome.jpg|right|250px]]". Captions are desirable, and are added at the end, after another vertical bar, as in “[[Image:Proteasome.jpg|thumb|A three-dimensional image of the proteasome]]", which appears at right.

For more details, see the tutorials Wikipedia:Picture tutorial, Wikipedia:Graphics tutorials, and Wikipedia:How to improve image quality.

The syntax for images is described here.

Sample Article

If you are unsure where to begin or what your article should look like, you can consider looking at already existing articles to get a feeling of what is expected. Some examples are Sic1, eIF2 and cdc6. Now a sample article follows which you can just copy-paste and use as a template for your own article. Notice that you do not need to fill in all the fields of the protein template, they will just not appear if you leave them empty.

{{protein
| Name = 
| image = 
| width = 
| caption =
| Symbol = 
| AltSymbols =
| ATC_prefix=
| ATC_suffix=
| ATC_supplemental=
| CAS_number=
| CAS_supplemental=
| DrugBank=
| EntrezGene = 
| HGNCid =
| OMIM = 
| PDB =
| RefSeq = 
| UniProt = 
| ECnumber = 
| Chromosome = 
| Arm = 
| Band = 
| LocusSupplementaryData = 
}}


'''Sic1''' is a [[protein]] in the budding yeast ''[[Saccharomyces cerevisiae]]''. 
It is a [[cyclin-dependent kinase]] (Cdk) inhibitor ... 
<ref name ="Tripodi"> 
{{cite journal 
| author = F. Tripodi, V. Zinzalla, M. Vanoni, L. Alberghina, P. Coccetti 
| date = 2007
| title = In CK2 inactivated cells ...
| journal = Biochemical and Biophysical Research Communication
| volume =  359 
| pages =   921-927
| pmid = 17574209 }}
</ref>

== Section 1 ==
[[Image:Sic1 fig1.jpg|thumb|400px|'''Fig. 1''' The diagram shows the role of Sic1]]

== Section 2 ==
=== Subsection ===
=== Subsection ===

== Section 3 ==
more information...

after the main text, your article should contain the following:


== See also ==
*[[p27 (gene)|p27]]
*[[CDKN1B]]

== References ==
<references/>

== External links ==
[http://www.page1.ch Page of Sic1]

<!--
This is a comment. Do not add categories to your article until it is finished; just 
[[Category:Cell cycle]]
[[Category:Genes]]
[[Category:Proteins]]
-->

Article structure

On Wikipedia there is no obligation to structure your article in any given way. Still it is helpful to see how other articles have done it and the article Wee1 provides a good reference:

Introduction
Function
Homologues
Regulation
Role in cancer
Mutant phenotype
See also
Notes
References
External links

Only the last four headings (See also,Notes,References, External links) should be in that order at the end of the article. And of course the introduction comes first.

Help

Here are some places you might want to go to if you need help

Wikiproject 1 Portal:Gene Wiki
Wikiproject 2 WP:MCB
User talk page of Hannes