Wikipedia talk:WikiProject Molecular Biology/Molecular and Cell Biology/Discussion Archive

message: What the hell is this (biocrawler.com)? Does anyone know anything about it? Why is this site using the Wiki design? Is Wikipedia going to have some freaky clones out there? -- Boris 14:38, 23 December 2005 (UTC)
replies: text: The "about" pages for that wiki are not very informative. You could try contacting the owner directly to try to find out what they hope to accomplish. --JWSchmidt 02:20, 24 December 2005 (UTC)
thread_title: Biocrawler

message: Hello,
Please notice this project. 
I hope that the List of publications in biology will be adopted by the molecular and cellular biology project.
Thanks,APH 06:50, 13 September 2005 (UTC)
thread_title:  [[Wikipedia:WikiProject Science pearls| Science pearls]]

message: I would like to finilize a solution to the lactase argument I been having with Boris and another transient over the issue of stating the difference between lactase and Beta galactosidase. Now I'm willing to agree to stating a brief 1-2 sentence statement on the Beta galactosidase and remove the affiliated statements for lactase, All I ask is that Boris and others agree and will not make a edit war over it. For others see discussion on lactase page for details.
:Heh, i totally forgot about this uhhh "edit war" we had there. So, BerserkerBen, what is your solution for the problem? -- Boris 21:22, 17 January 2006 (UTC)
replies: text: I think i stated it both there and here, already --BerserkerBen 23:57, 17 January 2006 (UTC)
thread_title: Lactase problem

message: Hi, there has been discussion about the quality of the various old lead images on the DNA article. I now created a new one, which you can see to the right. This picture is meant to give a general overview, it's not a "Structure of DNA"-chart (I'm still working on that). I'd appreciate any feedback! Mstroeck 03:34, 8 February 2006 (UTC)
replies: text: Good view of base pairing and minor/major grove.  What is that sticking out of the ribbons (apart from the nucleotides).  If it is the phophate group it is very misleading. The phophate is an integral part of the ribbon not attached to the ribbon as the diagram suggests. David D. (Talk) 08:54, 8 February 2006 (UTC)
replies: text: After looking at the close up i see you have superimposed the ribbon onto a ball and stick model (this should be described in the legend). Is it possible to only have the nucleotides and the ribbon, without the ball and stick backbone?  David D. (Talk) 08:59, 8 February 2006 (UTC)
replies: text: Well, the phosphate group, as I see it, is not "part of the ribbon". That's exactly what I was trying to avoid. There is no such thing as a "ribbon" in a physical DNA molecule, the ribbon is just a visual aid. Imagine for a second that you don't know the structure of DNA already and look at a chart with a flat ribbon and just the nucleotides. You'd have to read a caption to find out that there the backbone in reality consists of just the same "balls and sticks" that the rest of the molecule does. I'd rather leave out the ribbon completely than getting rid of the phosphates. Mstroeck 13:01, 8 February 2006 (UTC)
replies: text: I'm assuming you made this figure.  Do you have the structure ball and stick structure without the ribbon to compare?  Possibly you could have the two side by side. For me, the ribbon represents the backbone (obviously a cartoon that is not accurate), but the phosphates would be part of the cartoon ribbon. Is your point to show that the real backbone is not as smooth as a ribbon? David D. (Talk) 17:33, 8 February 2006 (UTC)
replies: text: Yes, that is my intent. I can't think of a way to make the backbone completely part of the ribbon without losing the immeadiacy of actually using balls and sticks to show that each strand is in fact a single molecule. I think that using just a ribbon is a bad idea and a confusing representation for people unfamiliar with the subject matter. I'll upload some alternative pictures, though. Mstroeck 21:47, 8 February 2006 (UTC)

text: I like the image and i like the ribbon too. But:- Could you make the ribbon transparent?- The image is too big > 900K. Not everyone has a good internet conection. If you cut the size in half that would make it ~300K. By the way all the amino acid images you have uploaded look very nice but they are huge in size. An amino acid image that is "200px" in size is as informative as a "900px" one.- Some of the phosphate groups look strange (DNA image). The ones circled in red have a bond between two Oxigen atoms. The phosphate group has a nice tetrahedral structure - those circled in blue don't seem to have one.- You love the green carbons, don't ya?- DNA can exists in 3 forms - A, B and Z. If you can make such an image for each of them that'll be great. -- Boris 22:24, 8 February 2006 (UTC)
thread_title:  New lead image for DNA 

message: Chaps, I'm having a difficult discussion on Talk:Diabetes mellitus on the role of chromium in insulin signalling. One editor there maintains that chromium influences insulin action independently from insulin receptor transduction, something that is only partially reported by the studies he quotes.
Could you kindly weigh in on this discussion, and also pass a verdict on the matter whether this issue is important enough to mention in the intro of an important health-related article. JFW | T@lk 15:45, 20 July 2006 (UTC)
thread_title:  Chromium in diabetes 

message: If everyone could please look here 
Now i think you guys will agree all of these articles should be combined in to ONE CELL CYCLE page...it makes no sense to have these seperate.
:It does make sence. Otherwise we would have 20 different terms pointing to the same article. How would then readers, who don't know what the terms mean, be expected to find what they are looking for? Can you solve this problem? Hmmm? -- Boris 05:03, 1 April 2006 (UTC)
thread_title:  Combine all the Articles 

message: Hi, I'm a member of the Wikipedia:Version_1.0_Editorial_Team, which is looking to identify quality articles in Wikipedia for future publication on CD or paper. We recently began assessing using these criteria, and we are looking for A-class, B-class, and Good articles, with no POV or copyright problems. Can you recommend any suitable articles? Please post your suggestions here. Cheers, Shanel 20:15, 9 March 2006 (UTC)
replies: text: I always use monobook and Firefox. --JWSchmidt 15:32, 20 December 2005 (UTC)
replies: text: Here's what i got. I created a script that inserts a search box called "mol-bio search" (MBS) between the "search" and the "toolbox" fields on the very left where the Wiki site links are. Right now MBS is very simple - it has a text field, a select filed with few simple options and a "submit" button. The string that is typed in the text filed is compared to the content in a small MySQL database and if a match is found it is displayed in a table. Well, you might say - why do that? Well if the reader types "fructose" in the wiki search box they can continue with either "Go" or "Search" - the first one sends the reader stright to the article, as long as there is one; the second one finds all the pages in wiki that have the word "fructose" in it and sorts them by relevancy. I don't like neither of them. Do you know how to use your "monobok.js" file? -- Boris 17:30, 22 December 2005 (UTC)
thread_title: Articles for the Wikipedia 1.0 project

message: What is the browser and the Wikipedia style that you (the members) use? I'm with Opera 7.5 and the "monobook" style. I'm asking because i'd like to show you what i've created and i need you opinion. Boris 13:58, 20 December 2005 (UTC)
replies: text: I always use monobook and Firefox. --JWSchmidt 15:32, 20 December 2005 (UTC)
replies: text: Here's what i got. I created a script that inserts a search box called "mol-bio search" (MBS) between the "search" and the "toolbox" fields on the very left where the Wiki site links are. Right now MBS is very simple - it has a text field, a select filed with few simple options and a "submit" button. The string that is typed in the text filed is compared to the content in a small MySQL database and if a match is found it is displayed in a table. Well, you might say - why do that? Well if the reader types "fructose" in the wiki search box they can continue with either "Go" or "Search" - the first one sends the reader stright to the article, as long as there is one; the second one finds all the pages in wiki that have the word "fructose" in it and sorts them by relevancy. I don't like neither of them. Do you know how to use your "monobok.js" file? -- Boris 17:30, 22 December 2005 (UTC)
thread_title: Hide/Show

message: I have an unpopular take on the protbox format. I believe that it should not be modular. I do agree, that modularity does offer the advatage of being easily adapted to different protein types which makes the current format appealing, but it also has a few disadvantages. The modular ability allows the various modules to be arranged in an ad hoc manner. A user creating a protbox is only forced to use the protbox start module, the remaining modules can be arranged in any order the creator chooses. This is counter to one of our goals which is to have a standard fomat for protein pages. The other disadvantage is the protbox creator needs to be aware of all the modules. The creator may not remember to include a module, even if they have information that can be used in a particular module. 
I believe that the taxobox is a nice example of any infobox that we can model protbox from. If one were to complete all the fields in a taxobox it is large, but one is not required to fill in all the fields. Only those fields that have information relevant to a species are displayed. Templates can be easily modified, and if new fields are required for a particular type/class of proteins a single protbox should be modified, instead of creating a new template. In addition, we can arrange the order of the fields, such that they appear in the same, logical order in all pages for all proteins. For example I believe the fields 'recent publications' and 'related articles' should be next to each other.
I have made a protbox sample that includes all the fields on the main project page (except for the Template:Protbox codes because I feel that as it stands it needs revision).  I think it should have functionality like the Template:Protein). I propose that we deprecate the current format and adopt a single protbox template. I made two examples using my proposed change to the template one using  the Myoglobin example and the other using a protein missing some of the fields (such as image). They can be found at :User:GAThrawn22/Sandbox/. I also made an example of a hormone(insulin) and an enzyme(alpha ketoglutarate) they can be found at: User:GAThrawn22/Sandbox/protboxtest2. The code for the template can be found at User:GAThrawn22/Sandbox/protboxtest. I will be adding some other fields if others agree with my proposition. Tell me what you guys think. -- GAThrawn22 01:27, 29 June 2006 (UTC)
replies: text: I propose an infobox which takes advantage of the new parserfunctions capability... With this i could put together a template which only displays sections which have information filled in for... Ill make a sandbox version at some point in the next week to illustrate this. Zephyris 16:02, 11 August 2006 (UTC)
replies: text: Thanks for the suggestion. The protbox was already created using the parser function capability, so only those fields that have information in them is visible. A description of its usage can be found at: Wikipedia:WikiProject Molecular and Cellular Biology/protbox usage, while the template can be found at: Template:Protbox. if you have experience using parser functions and creating templates, and you have any suggestions for modifications your help is welcomed. Thanks again. GAThrawn22 00:16, 12 August 2006 (UTC)
replies: text: Awesome, though the wikiproject page needs updating to change it from the current modular style infobox. Im also preparing a section for better representation of enzymatic reactions, see my work in progress wikiproject/templates wikipedia:wikiproject metabolic pathways. 80.225.195.54 13:23, 12 August 2006 (UTC)
replies: text: Lol, not signed in and cant do links... Wikipedia:Wikiproject Metabolic PathwaysZephyris 13:31, 12 August 2006 (UTC)
thread_title: Propsed Infobox format change

message: Each compound has L- and D-isoforms, which chemically are indistinguishable, but biologically they are totally different. Are we going to have two articles for each one or just one article for both? BorisTM 13:49, 9 November 2005 (UTC)
thread_title: L- and D-isoforms

message: ====Adherins====
What are these proteins? I know about "Adhesins" and "Cadherins", but "Adherins". Any links? PubMed gives only 5 search results.The article was created by an anonymous user. -- Boris 15:04, 6 January 2006 (UTC)
replies: text: Maybe they meant "adherens", as in macula adherens? --Arcadian 16:58, 6 January 2006 (UTC)
replies: text: "macula adherens" is in Latin. Most probably the person who wrote the article got "Adhesins" and "Cadherins" all mixed up. And besides the whole article doesn't make sence. It is some mumbo-jumbo sh!t, i'll delete right now untill they provide sources and better writing. -- Boris 17:57, 6 January 2006 (UTC)
thread_title: Types

message: What are these proteins? I know about "Adhesins" and "Cadherins", but "Adherins". Any links? PubMed gives only 5 search results.The article was created by an anonymous user. -- Boris 15:04, 6 January 2006 (UTC)
replies: text: Maybe they meant "adherens", as in macula adherens? --Arcadian 16:58, 6 January 2006 (UTC)
replies: text: "macula adherens" is in Latin. Most probably the person who wrote the article got "Adhesins" and "Cadherins" all mixed up. And besides the whole article doesn't make sence. It is some mumbo-jumbo sh!t, i'll delete right now untill they provide sources and better writing. -- Boris 17:57, 6 January 2006 (UTC)
thread_title: Adherins

message: Could someone review cholesterylester transfer protein for me and add what is necessary? JFW | T@lk 23:48, 17 November 2005 (UTC)
thread_title: CETP