Talk:Materials - Revision history

Kathryn Muratore at 17:42, 26 May 2011

Kathryn Muratore — Thu, 26 May 2011 17:42:25 GMT

←Older revision		Revision as of 17:42, 26 May 2011
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	If anyone has an interest in assisting, either by providing input to the equipment category definitions or with requirements related to them, please contact me via external email(bill at openwetware dot org) or via [[Special:Emailuser/Bill Flanagan\|OWW email]]. You can also leave comments either [[Talk:Materials\|here]] or on		If anyone has an interest in assisting, either by providing input to the equipment category definitions or with requirements related to them, please contact me via external email(bill at openwetware dot org) or via [[Special:Emailuser/Bill Flanagan\|OWW email]]. You can also leave comments either [[Talk:Materials\|here]] or on
	[[User talk:Bill_Flanagan\|my talk page]].		[[User talk:Bill_Flanagan\|my talk page]].
		+
		+	===Category Add===
		+	*Label for this suggestion: New top level category for DNA (and RNA?)
		+	*Related to Label:
		+	*Author:[[User:Kathryn Muratore\|Kathryn Muratore]] 13:42, 26 May 2011 (EDT)
		+	*Proposed New Material Category Name: nucleic acids
		+	*Descending-from Existing Parent Category Name:
		+	*Description:
		+	*Comments:
		+	*End of Add
		+
		+	===Category Add===
		+	*Label for this suggestion: New subcategory for RNA
		+	*Related to Label:
		+	*Author:[[User:Kathryn Muratore\|Kathryn Muratore]] 13:42, 26 May 2011 (EDT)
		+	*Proposed New Material Category Name: RNA
		+	*Descending-from Existing Parent Category Name: nucleic acids
		+	*Description:
		+	*Comments:Not sure how helpful/relevant this category is.
		+	*End of Add
		+
		+	===Category Add===
		+	*Label for this suggestion: New subcategory for DNA
		+	*Related to Label:
		+	*Author:[[User:Kathryn Muratore\|Kathryn Muratore]] 13:42, 26 May 2011 (EDT)
		+	*Proposed New Material Category Name: DNA
		+	*Descending-from Existing Parent Category Name: nucleic acids
		+	*Description:
		+	*Comments: This is already a category, but it's not listed on the materials category tree that I can find above.
		+	*End of Add
		+
		+	===Category Add===
		+	*Label for this suggestion: New DNA subcategory for empty vectors
		+	*Related to Label:
		+	*Author:[[User:Kathryn Muratore\|Kathryn Muratore]] 13:42, 26 May 2011 (EDT)
		+	*Proposed New Material Category Name: cloning vectors (empty)
		+	*Descending-from Existing Parent Category Name: DNA
		+	*Description: Custom or commercial plasmids, BACs, YACs, etc... for cloning.
		+	*Comments: There is an Escherichia coli/Vectors section under the E coli category, but I see this as more analogous to the Restriction Enzymes category. Although commercial vectors can be linked to off-site, the ease of using intra-wiki links makes this desirable from my perspective. "Vectors" is already a page in the DNA category, but it is not a materials category.
		+	*End of Add
		+
		+	===Category Add===
		+	*Label for this suggestion: New DNA subcategory for vectors with inserts
		+	*Related to Label:
		+	*Author:[[User:Kathryn Muratore\|Kathryn Muratore]] 13:42, 26 May 2011 (EDT)
		+	*Proposed New Material Category Name: cloned genes
		+	*Descending-from Existing Parent Category Name: DNA
		+	*Description: Gene constructs used in the research on the OWW site.
		+	*Comments: Separating this from empty vectors will help limit clutter. This can also be helpful for molecular biologists to contact each other to use their constructs even if it is not yet (peer-review) published.
		+	*End of Add

Rhodri Harfoot: /* Suggested Ontology List (Please add Here!) */

Rhodri Harfoot — Thu, 14 May 2009 04:50:54 GMT

Suggested Ontology List (Please add Here!)

←Older revision		Revision as of 04:50, 14 May 2009
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	=== Suggested Ontology List (Please add Here!) ===		=== Suggested Ontology List (Please add Here!) ===
		+	'''[[User:Rhodri Harfoot\|Rhodri Harfoot]] 00:50, 14 May 2009 (EDT)''' Chemicals organised by IUPAC name with common name/abbreviation in brackets

	== Category Information Template Page: Input required! ==		== Category Information Template Page: Input required! ==

Bill Flanagan: /* Equipment */

Bill Flanagan — Wed, 29 Apr 2009 17:58:27 GMT

Equipment

←Older revision		Revision as of 17:58, 29 April 2009
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	: I'm very much in favour of another top level page for equipment. We should probably shouldn't put it into the menu frame on the left until the content is mature. Together with consumables (=material) and protocols, it should be the 3rd major category of information on OWW. [[User:Jakob Suckale\|Jakob Suckale]] 12:58, 29 April 2009 (EDT)		: I'm very much in favour of another top level page for equipment. We should probably shouldn't put it into the menu frame on the left until the content is mature. Together with consumables (=material) and protocols, it should be the 3rd major category of information on OWW. [[User:Jakob Suckale\|Jakob Suckale]] 12:58, 29 April 2009 (EDT)
		+
		+	[[User:Bill Flanagan\|Bill Flanagan (OpenWetWare.org at MIT)]] 13:58, 29 April 2009 (EDT)**100% agreement. I'm not proceeding to even revisit protocols until material is in better shape.

	==Volunteers==		==Volunteers==

Jakob Suckale: /* Equipment */

Jakob Suckale — Wed, 29 Apr 2009 17:00:09 GMT

Equipment

←Older revision		Revision as of 17:00, 29 April 2009
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	I'm also interested in creating a new top-level page for equipment. I'm starting to collect the existing info in OWW that can be used as the basis for such a taxonomy. I don't want to go crazy defining a large empty set of categories; in fact, a goal would be to make sure than any new category contains at least one member or is a branch leading to a member. OWW seems to be much more about the 'what is' of the lab and not a format definition of what a lab could or should be. In that regard, using an external set of categories for something like equipment could be a good idea as long as only the items in the taxonomy that are in use are elevated to formal OWW categories. This implies a virtual taxonomy that 'will exist' as well as a real taxonomy that 'current does exist' within OWW.		I'm also interested in creating a new top-level page for equipment. I'm starting to collect the existing info in OWW that can be used as the basis for such a taxonomy. I don't want to go crazy defining a large empty set of categories; in fact, a goal would be to make sure than any new category contains at least one member or is a branch leading to a member. OWW seems to be much more about the 'what is' of the lab and not a format definition of what a lab could or should be. In that regard, using an external set of categories for something like equipment could be a good idea as long as only the items in the taxonomy that are in use are elevated to formal OWW categories. This implies a virtual taxonomy that 'will exist' as well as a real taxonomy that 'current does exist' within OWW.

-	: I'm very much in favour of another top level page for equipment. We should probably shouldn't put it into the menu frame on the left until the content is mature. [[User:Jakob Suckale\|Jakob Suckale]] 12:58, 29 April 2009 (EDT)	+	: I'm very much in favour of another top level page for equipment. We should probably shouldn't put it into the menu frame on the left until the content is mature. Together with consumables (=material) and protocols, it should be the 3rd major category of information on OWW. [[User:Jakob Suckale\|Jakob Suckale]] 12:58, 29 April 2009 (EDT)

	==Volunteers==		==Volunteers==

Jakob Suckale: /* Equipment */

Jakob Suckale — Wed, 29 Apr 2009 16:58:39 GMT

Equipment

←Older revision		Revision as of 16:58, 29 April 2009
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	I'm also interested in creating a new top-level page for equipment. I'm starting to collect the existing info in OWW that can be used as the basis for such a taxonomy. I don't want to go crazy defining a large empty set of categories; in fact, a goal would be to make sure than any new category contains at least one member or is a branch leading to a member. OWW seems to be much more about the 'what is' of the lab and not a format definition of what a lab could or should be. In that regard, using an external set of categories for something like equipment could be a good idea as long as only the items in the taxonomy that are in use are elevated to formal OWW categories. This implies a virtual taxonomy that 'will exist' as well as a real taxonomy that 'current does exist' within OWW.		I'm also interested in creating a new top-level page for equipment. I'm starting to collect the existing info in OWW that can be used as the basis for such a taxonomy. I don't want to go crazy defining a large empty set of categories; in fact, a goal would be to make sure than any new category contains at least one member or is a branch leading to a member. OWW seems to be much more about the 'what is' of the lab and not a format definition of what a lab could or should be. In that regard, using an external set of categories for something like equipment could be a good idea as long as only the items in the taxonomy that are in use are elevated to formal OWW categories. This implies a virtual taxonomy that 'will exist' as well as a real taxonomy that 'current does exist' within OWW.
		+
		+	: I'm very much in favour of another top level page for equipment. We should probably shouldn't put it into the menu frame on the left until the content is mature. [[User:Jakob Suckale\|Jakob Suckale]] 12:58, 29 April 2009 (EDT)

	==Volunteers==		==Volunteers==

Bill Flanagan at 12:56, 28 April 2009

Bill Flanagan — Tue, 28 Apr 2009 12:56:52 GMT

←Older revision		Revision as of 12:56, 28 April 2009
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	B.		B.
		+
		+	==More Information==
		+	[[User:Bill Flanagan\|Bill Flanagan (OpenWetWare.org at MIT)]] 08:56, 28 April 2009 (EDT) I'm deploying the new category tools in test today and in production over the next few days. I held off until I completed a blog entry to describe it and (hopefully) to provide info to members on how to use it. My goal is to make this sufficiently transparent to allow uses with good lab and research experience but limited wiki markup experience to make entries. One issue I'm looking for help here and elsewhere in is a way to maintain the category trees themselves. When you make a new category, how does it relate to an existing one? In particular, there's no clear-cut way of handling aliases or even recognizing they exist. One way is to merge two categories into one by making one category a redirect to a more well accepted term. As to which of two terms is the primary one and which is an alias is a matter that will probably be determined by context or the member who puts more into providing the information. The category pages can be uses to show their place in a hierarchy. The category tree extension also does a great job at this. I know there are better ways but for now I'm trying to get something moving then make it perfect later.
		+
		+	==Equipment==
		+
		+	I'm also interested in creating a new top-level page for equipment. I'm starting to collect the existing info in OWW that can be used as the basis for such a taxonomy. I don't want to go crazy defining a large empty set of categories; in fact, a goal would be to make sure than any new category contains at least one member or is a branch leading to a member. OWW seems to be much more about the 'what is' of the lab and not a format definition of what a lab could or should be. In that regard, using an external set of categories for something like equipment could be a good idea as long as only the items in the taxonomy that are in use are elevated to formal OWW categories. This implies a virtual taxonomy that 'will exist' as well as a real taxonomy that 'current does exist' within OWW.
		+
		+	==Volunteers==
		+
		+	If anyone has an interest in assisting, either by providing input to the equipment category definitions or with requirements related to them, please contact me via external email(bill at openwetware dot org) or via [[Special:Emailuser/Bill Flanagan\|OWW email]]. You can also leave comments either [[Talk:Materials\|here]] or on
		+	[[User talk:Bill_Flanagan\|my talk page]].

Bill Flanagan: /* automatic link collection */

Bill Flanagan — Thu, 23 Apr 2009 23:02:50 GMT

automatic link collection

←Older revision		Revision as of 23:02, 23 April 2009
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	I'm using the email message you sent today as a basis for continuing this effort.		I'm using the email message you sent today as a basis for continuing this effort.
		+
		+	==More Search Information==
		+
		+	[[User:Bill Flanagan\|Bill Flanagan (OpenWetWare.org at MIT)]] 19:02, 23 April 2009 (EDT)Still at it. I've now created a sort of generalized extension that will allow us to add searches like the Google Suggest search for any namespace. I've removed it from the core MediaWiki code I hacked it together with originally and now rolled it into a parser tag extension.
		+
		+	I'm now doing the same (generalizing) a way to allow adding new categories to any page without opening the page for editing. You do need to be logged in but it's still a lot more convenient. If you do choose to add category tags, they will still work but this clearly will be the way to do it.
		+
		+	I'm also thinking about introducing a way to view protocol and material information as a formal namespace. That would mean you will be able to apply the protocol: and material: tag to a search. This will allow us to organize the display of this information as it relates to those terms. It's a sort of shortcut but it may be useful. To make it work we need to apply a more rigorous rating function to the OWW content than a simple full text search. I'm investigating how to do this now. A good bet is to follow what academics and some companies are doing to organize the content of Wikipedia. What's good for the goose...
		+
		+	I should have the new linking in place within the next week. I'm also going to contribute the extension to MediaWiki: it's a good solution to a lot of sites problems using search within MediaWiki.
		+
		+	I'm also adding support to allow people to subscribe to Material and Protocol categories. Any page including those categories will be added to their watch list. This is a good time to also roll out work I did with [[User:Jason R. Kelly\|Jason Kelly]] to define a way to include a list of someone else's watchlist pages and now some categories to their own watchlist.
		+
		+	I'll expand upon this list as I deploy the mods in a set of Community blog entries.
		+
		+	B.

Bill Flanagan: /* automatic link collection */

Bill Flanagan — Thu, 16 Apr 2009 18:55:22 GMT

automatic link collection

←Older revision		Revision as of 18:55, 16 April 2009
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	Best, [[User:Jakob Suckale\|Jakob Suckale]] 11:18, 6 April 2009 (EDT)		Best, [[User:Jakob Suckale\|Jakob Suckale]] 11:18, 6 April 2009 (EDT)
		+
		+	[[User:Bill Flanagan\|Bill Flanagan (OpenWetWare.org at MIT)]] 14:55, 16 April 2009 (EDT) Jakob, Protocols and materials do work differently but new materials do get added to the Materials page automatically. The difference is the content of the Material page relies upon using Categories. These are the tags at the bottom of the page. Any page that has a 'Material' category will be listed here. The tag is located in the page text generally on the last line. It looks like this:
		+
		+	'''<nowiki>[[Category:Material]]</nowiki>'''
		+
		+	Just to make sure people know that the categories are there, I added a sidebar box that shows the list of documents contained in documents. You can follow the category link to a page where all the docs that are part of that category are shown sorted alphabetically.
		+
		+	Per your comments, we need to show more people how they work. Materials is at least consistent in the way the links are created. But if people don't use the Category tags in the document, they will not show up.
		+
		+	Thanks for pointing this out. The box on the sidebar is a crude but hopefully useful first step in making a generally more useful set of tools.
		+
		+	I'm using the email message you sent today as a basis for continuing this effort.

Jakob Suckale: moved old comment into body of page

Jakob Suckale — Thu, 16 Apr 2009 12:10:32 GMT

moved old comment into body of page

←Older revision		Revision as of 12:10, 16 April 2009
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		+	== restyled ==
	*'''[[User:Bcanton\|BC]] 13:13, 4 June 2006 (EDT)''':I put together a [[Materials/Template\|template page]] for materials similar to the [[Protocols/Template\|protocols template]] written by [[Reshma Shetty]].		*'''[[User:Bcanton\|BC]] 13:13, 4 June 2006 (EDT)''':I put together a [[Materials/Template\|template page]] for materials similar to the [[Protocols/Template\|protocols template]] written by [[Reshma Shetty]].

-	~~'''~~This is a proposed restyling of the materials page. I thought I would put it here to see what people thought before making it go live on the real page. Comments welcome. I just thought the page could be made more compact and easy to view. Feel free to retweak if you have a better idea. A similar thing could be done to the protocols page. My only concern is whether it makes it more difficult/intimidating for those new to wikis to edit? Which is definitely not what I want.~~'''~~ --[[Reshma Shetty \| RS]]	+	This is a proposed restyling of the materials page. I thought I would put it here to see what people thought before making it go live on the real page. Comments welcome. I just thought the page could be made more compact and easy to view. Feel free to retweak if you have a better idea. A similar thing could be done to the protocols page. My only concern is whether it makes it more difficult/intimidating for those new to wikis to edit? Which is definitely not what I want. --[[Reshma Shetty \| RS]]
	*'''[[User:Jennyn\|Jennyn]] 16:58, 26 February 2006 (EST)''': The page has been restylized. Please feel free to edit as you feel necessary.		*'''[[User:Jennyn\|Jennyn]] 16:58, 26 February 2006 (EST)''': The page has been restylized. Please feel free to edit as you feel necessary.
-
-	~~== automatic link collection ==~~
-
-	The materials page unlike the [[protocols]] page still does not collect pages according to their tag. I think this is a very useful feature, since new materials pages would then appear here without an additional edit to the materials page. This should be set up for this page as well.
-
-	~~Best, [[User:Jakob Suckale\|Jakob Suckale]] 11:18, 6 April 2009 (EDT)~~
-

	== Proposed Changes to Materials Page ==		== Proposed Changes to Materials Page ==
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	Please make any suggestions here for changing the process we're proposing/crafting. If we use standard formats during this process, we can both handle suggestions about process as specific changes are made in the hierarchy.		Please make any suggestions here for changing the process we're proposing/crafting. If we use standard formats during this process, we can both handle suggestions about process as specific changes are made in the hierarchy.
		+
		+	== automatic link collection ==
		+
		+	The materials page unlike the [[protocols]] page still does not collect pages according to their tag. I think this is a very useful feature, since new materials pages would then appear here without an additional edit to the materials page. This should be set up for this page as well.
		+
		+	Best, [[User:Jakob Suckale\|Jakob Suckale]] 11:18, 6 April 2009 (EDT)

Bill Flanagan at 16:35, 15 April 2009

Bill Flanagan — Wed, 15 Apr 2009 16:35:55 GMT

←Older revision		Revision as of 16:35, 15 April 2009
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	<div style="padding: 2px">[[Image:OWWMaterials.png]]</div>		<div style="padding: 2px">[[Image:OWWMaterials.png]]</div>
	<hr class="divider">		<hr class="divider">
		+
		+
		+	*[[User:Bill Flanagan\|Bill Flanagan (OpenWetWare.org at MIT)]] 12:35, 15 April 2009 (EDT)Check out what we're up to regarding making the OWW Materials section more useful. [[User:Jakob Suckale\|Jakob Suckale]] brought this to my attention a while back. I've been working on a number of related enhancements to OWW to make upgrades to the way we enter and categorize information about them. The [[Protocols]] page does a better job at aggregating content. But it also is in need of improvements. Rather than presuppose tools, I'm interested in seeing how we can make them up as we move forward to get the most out of the members of OWW.
		+

	*'''[[User:Bcanton\|BC]] 13:13, 4 June 2006 (EDT)''':I put together a [[Materials/Template\|template page]] for materials similar to the [[Protocols/Template\|protocols template]] written by [[Reshma Shetty]].		*'''[[User:Bcanton\|BC]] 13:13, 4 June 2006 (EDT)''':I put together a [[Materials/Template\|template page]] for materials similar to the [[Protocols/Template\|protocols template]] written by [[Reshma Shetty]].
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	Best, [[User:Jakob Suckale\|Jakob Suckale]] 11:18, 6 April 2009 (EDT)		Best, [[User:Jakob Suckale\|Jakob Suckale]] 11:18, 6 April 2009 (EDT)
		+
		+
		+	== Proposed Changes to Materials Page ==

	[[User:Bill Flanagan\|Bill Flanagan (OpenWetWare.org at MIT)]] 11:40, 6 April 2009 (EDT)This is a good idea. We've discussed redoing the protocols page for a long time but to date it's still 'the same as it ever were'. I'll be glad to participate (i.e., provide technical assistance as needed) in the work if someone can help work on the requirements:		[[User:Bill Flanagan\|Bill Flanagan (OpenWetWare.org at MIT)]] 11:40, 6 April 2009 (EDT)This is a good idea. We've discussed redoing the protocols page for a long time but to date it's still 'the same as it ever were'. I'll be glad to participate (i.e., provide technical assistance as needed) in the work if someone can help work on the requirements: