User:Chris Day/sandbox1: Difference between revisions

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This is a work in progress.  Feel free to edit it here or make comments on the talk page.
==Positive selection on the human genome==
Vallender EJ, Lahn BT.
Hum Mol Genet. 2004 Oct 1;13 Spec No 2:R245-54. Review.
PMID 15358731


=Proposal for Subgroups=
Genetically engineered mice with an additional class of cone photoreceptors: implications for the evolution of color vision.
==Overview==
Smallwood PM, Olveczky BP, Williams GL, Jacobs GH, Reese BE, Meister M, Nathans J.
Subgroups can represent a subset of editors and authors from a workgroup with a niche interest, be a vehicle for collaboration between different workgroups, a navigation tool or all of these concepts.
Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11706-11. Epub 2003 Sep 19.
PMID 14500905


==Rationale==
The evolution of trichromatic color vision by opsin gene duplication in New World and Old World primates.
The breadth of some workgroups is huge, so it makes sense to break them down into more natural subgroups.  Within biology and engineering alone whole academic departments can be based on a subset of those workgroups disciplines, ''i.e.'' Botany.  
Dulai KS, von Dornum M, Mollon JD, Hunt DM.
Genome Res. 1999 Jul;9(7):629-38.
PMID 10413401


There is also an interdisciplinary need for subgroups. Take a hypothetical subgroup called Biochemistry Subgroup, it should involve editors and authors from at least three different workgroups, Health Sciences, Biology and the Chemistry Workgroup.
Identification of a variant associated with adult-type hypolactasia.
Enattah NS, Sahi T, Savilahti E, Terwilliger JD, Peltonen L, Järvelä I.
Nat Genet. 2002 Feb;30(2):233-7. Epub 2002 Jan 14.
PMID 11788828


A further advantage is that readers will be able to use the Subgroup categories to focus on articles in a particular discipline. An electrical engineer can first look at the Electrical Engineering Subgroup category. A military historian can first look at the Military History Subgroup category. A thermodynamics student can first look at the Thermodynamics Subgroup category. Those readers will find it harder to find specific articles somewhere amidst a great many articles in the Engineering category or the History category or the Chemistry category. Obviously related articles subpages will serve these readers better as they get tuned to citizendiums other navigation tools but as a first bite these Subgroup categories will serve as an effective corral for some topics.
==RNAi-mediated pathways.==


==The genesis of a subgroup==
RNAi-mediated pathways in the nucleus.
Workgroups are a collection of topic areas in citizendium that rarely change. To add a new workgroup requires top down approval. In contrast, the number and names of various subgroups should be more fluid within the limitation that one cluster can only be in up to three different subgroups (this will limit the narrowness of subgroups).
Matzke MA, Birchler JA.
Nat Rev Genet. 2005 Jan;6(1):24-35. Review.
PMID 15630419


===Who can start a subgroup?===
A structural-maintenance-of-chromosomes hinge domain-containing protein is required for RNA-directed DNA methylation.
Authors and editors can initiate any subgroup idea but it will be up to each workgroups editors to recognise and endorse "affiliated" subgroups. This is preferable to having to go as high as the editorial council, as with requests for new workgroups. This bottom up approach should encourage the creation of experimental subgroups and lead to fertile collaborations within citizendium.
Kanno T, Bucher E, Daxinger L, Huettel B, Böhmdorfer G, Gregor W, Kreil DP, Matzke M, Matzke AJ.
Nat Genet. 2008 May;40(5):670-5. Epub 2008 Apr 20.
PMID 18425128


===Which subgroups are needed?===
Target mimicry provides a new mechanism for regulation of microRNA activity.
Editors decide which subgroups are relevant and will add the appropriate ones to their workgroup (see an explanation on how to use the A-D parameters below in section "How to start a Subgroup"). If editors from another workgroup feel there is an interdisciplinary connection, they too might consider adding their workgroup to the subgroup template. Subgroups may well come and go in a Darwinian manner depending on the various interests of editors and authors and whether it is affiliated with any workgroup.
Franco-Zorrilla JM, Valli A, Todesco M, Mateos I, Puga MI, Rubio-Somoza I, Leyva A, Weigel D, García JA, Paz-Ares J.
Nat Genet. 2007 Aug;39(8):1033-7. Epub 2007 Jul 22.
PMID 17643101


===How do we prevent redundancy?===
Cell cycle control of centromeric repeat transcription and heterochromatin assembly.
We need a mechanism to prevent redundancy.  ''i.e.'' we may not want two similar subgroups such as Protein Structure Subgroup and Macromolecule Structure Subgroup. At present this would probably be an informal process but could require a more formal process as the citizendium community grows.
Chen ES, Zhang K, Nicolas E, Cam HP, Zofall M, Grewal SI.
 
Nature. 2008 Feb 7;451(7179):734-7. Epub 2008 Jan 23.
==Implementation==
PMID 18216783
The subgroup name will be added to the metadata of any article falling under the umbrella of that particular subgroup of authors. This idea is currently active and seen in the metadata template as the three fields of sub1, sub2 and sub3. These fields can be used to denote the affiliation of any article cluster; up to three different subgroups can be added per cluster. An example edit can be seen at the [http://en.citizendium.org/wiki?title=Template:Chemical_engineering/Metadata&diff=prev&oldid=100293203 Chemical engineering article] where the [[:Category:Chemical Engineering Subgroup]] is being used as a pilot for this idea.
 
===The subgroups home===
The home for each subgroup will be at 'CZ:NAME subgroup' and there will be a 'Category:NAME subgroup' page that lists all the articles within the subgroup, where NAME is the desired subgroup name.
 
===How to start a subgroup===
1) Create a template titled Template:NAME Subgroup.
 
2) Add the following to the template:  <nowiki>{{Subgroup|NAME|A|B|C|D}}</nowiki>. A-D are four optional parameters that can be added by editors to affiliate their Workgroup with the subgroup.
 
Thus, [http://en.citizendium.org/wiki?title=Template:Chemical_Engineering_Subgroup&action=edit Template:Chemical Engineering Subgroup] has <nowiki>{{Subgroup|Chemical Engineering|Engineering|Chemistry}}</nowiki> in the body of the template.
 
3) The template <nowiki>{{NAME Subgroup}}</nowiki> should be placed at the top of the CZ home page for the subgroup and its talk page as well as each category in the subgroup. For example, our [[CZ:Chemical_Engineering_Subgroup|model subgroup]] currently has the following pages:
 
:CZ:Chemical Engineering Subgroup
:CZ talk:Chemical Engineering Subgroup
:Category:Chemical Engineering Subgroup
:Category:Chemical Engineering Approved
:Category:Chemical Engineering Editors
:Category:Chemical Engineering Authors
:Category:Chemical Engineering tag
 
Any categories at the foot of a page and/or descriptive text for each page is automatically added based on the parameters A-D.
 
===How to navigate subgroup pages===
The navigation bar at the top will lead one to all the relevant pages using standard hyperlinks.
{{Image|Subgroup navigation.jpg|center|600px}}
 
Each affiliated Workgroup is hyperlinked in the subpages navigation header and an  affiliated workgroup category is placed at the foot of the CZ:Subgroup home (See an example of the affiliated subgroups category for the engineering workgroup at [[:Category:Engineering Affiliated Subgroups]]).  This type of category will be used to track all the subgroups that affiliate with any given workgroup.
 
===How to customize subgroup headers===
Each subgroup will have a grey coloured navigation bar by default.  See the genetics [[:Category:Genetics_Subgroup|example here]].  It is possible, however, to have a jazzy workgroup banner at the top ''IF'' there is an image at the location "Image:NAME banner.jpg" where NAME refers to the subgroup name. I have made one for Chemical Engineering as a trial run, see the header banner at the [[CZ:Chemical_Engineering_Subgroup|home page]] for the subgroup. Also see below:
 
{{Image|Chemical_Engineering banner.jpg|center|600px|Example of a Subgroup specific banner.}}
 
===How to invite your colleagues===
Authors and Editors can be added to a Subgroup by adding the appropriate category tags to their user page (either <nowiki>{{Category:NAME Editor}} or {{Category:NAME Author}}</nowiki>, where NAME refers to the subgroup name). Anyone can add themselves as an author, of course.
 
It should be noted that the editor label does not give special editorial rights outside their designated workgroup! It is merely to identify members of the subgroup that are editors in one or more workgroups. Note: there may well be clusters tagged in the Subgroups collection that a "subgroup editor" cannot recommend for approval.
 
==Summary==
Since the pilot [[CZ:Chemical Engineering Subgroup|Chemical Engineering Subgroup]] was initiated it has added 112 articles and 16 of them have been approved. Of those 112 articles they include content that is overlapping with the Engineering, Chemistry, Physics and Earth Sciences Workgroups demonstrating the potential for interdisciplinary collaborations within the environment of a Subgroup.

Revision as of 12:07, 20 January 2009

Positive selection on the human genome

Vallender EJ, Lahn BT. Hum Mol Genet. 2004 Oct 1;13 Spec No 2:R245-54. Review. PMID 15358731

Genetically engineered mice with an additional class of cone photoreceptors: implications for the evolution of color vision. Smallwood PM, Olveczky BP, Williams GL, Jacobs GH, Reese BE, Meister M, Nathans J. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11706-11. Epub 2003 Sep 19. PMID 14500905

The evolution of trichromatic color vision by opsin gene duplication in New World and Old World primates. Dulai KS, von Dornum M, Mollon JD, Hunt DM. Genome Res. 1999 Jul;9(7):629-38. PMID 10413401

Identification of a variant associated with adult-type hypolactasia. Enattah NS, Sahi T, Savilahti E, Terwilliger JD, Peltonen L, Järvelä I. Nat Genet. 2002 Feb;30(2):233-7. Epub 2002 Jan 14. PMID 11788828

RNAi-mediated pathways.

RNAi-mediated pathways in the nucleus. Matzke MA, Birchler JA. Nat Rev Genet. 2005 Jan;6(1):24-35. Review. PMID 15630419

A structural-maintenance-of-chromosomes hinge domain-containing protein is required for RNA-directed DNA methylation. Kanno T, Bucher E, Daxinger L, Huettel B, Böhmdorfer G, Gregor W, Kreil DP, Matzke M, Matzke AJ. Nat Genet. 2008 May;40(5):670-5. Epub 2008 Apr 20. PMID 18425128

Target mimicry provides a new mechanism for regulation of microRNA activity. Franco-Zorrilla JM, Valli A, Todesco M, Mateos I, Puga MI, Rubio-Somoza I, Leyva A, Weigel D, García JA, Paz-Ares J. Nat Genet. 2007 Aug;39(8):1033-7. Epub 2007 Jul 22. PMID 17643101

Cell cycle control of centromeric repeat transcription and heterochromatin assembly. Chen ES, Zhang K, Nicolas E, Cam HP, Zofall M, Grewal SI. Nature. 2008 Feb 7;451(7179):734-7. Epub 2008 Jan 23. PMID 18216783

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