Let's make the SEQwiki even more awesome

marcowanger · 09-14-2011, 12:51 PM

Help make the Wiki awesome!

The SEQanswers wiki (or "SEQwiki" for short) is a great help for users of this forum: It's a catalog of high-throughput sequencing tools. There is currently an effort to get the SEQanswers forum and the wiki published in the next NAR database issue. This is a great opportunity to get the wiki in shape: Some of the tool descriptions are just "stubs", but in order for those pages to be really helpful, we need just ten minutes of your time.

We invite everyone to pick one (or of course more!) tools that she or he uses and improve its description in the wiki. If you are the author of the tool, it is the best time to advertise there by writing concise description to help people choose the RIGHT tools. This will help others tremendously when they decide which tool to use. It's also the perfect opportunity to write down the sometimes annoying things that are often not mentioned on the homepages of those tools.

Here are some suggestions what you could write about your tool:

Which tasks is the tool good at? (something like: "really fast read mapping")
What are the limitations? In which situations would the tool not be appropriate? ("cannot find indels", "needs at least least 32 GB RAM")

Are there any pitfalls? Any idiosyncrasies when using the tool? ("be careful: if the input file is corrupt, there's no error message -- and the results will even look meaningful"). Hidden requirement? e.g. that said memory efficient but require 32GB or more for a reasonable small dataset?

Which alternative tools exist? ("if you still use MAQ, you should switch to BWA")
Are there related tools? (on the BWA page: "Seal uses the BWA algorithm, but runs on a Hadoop cluster")

Since the wiki is there to help us decide which tool to use for a specific purpose, please also try to update the tags for your tool. Just try to make it fit into the "Browse software" page!

While you are editing and using the wiki, please also let us know about any issues you have with the wiki software itself -- things perhaps only an administrator can change.

Do any templates look ugly?

Is the navigation too confusing?

Don't like the fonts?

We cannot promise to take care of everything, but please tell us!

Writing by M Martin. Thanks!

The SeqWiki Publishing team want to thank you for the help

marcowanger · 09-14-2011, 01:08 PM

Dear all, in the meantime, please be reminded

Bioinformatics method means METHOD employed. Most of the existing tags are fine.

Biological domain refers to something bigger. e.g. Genomics, Transcriptomics, Chip-Seq, etc. Please don't tag Alignment as domains.

I am not sure if tag is case-sensitive. If we assume it is not. Please start with the tag with a capital letter.

Alignment NOT alignment

If the word is two word, please make it two. For example "Method" Base Call, not basecall

Please correct me if the case is case-insensitive

Thanks a lot

krobison · 09-14-2011, 01:25 PM

Tags are case (and punctuation!) sensitive and currently are sorted so that uppercase comes first and lowercase later. So "Assembly Visualization" will be soon followed by "Assembly visualization", but "assembly visualization" will be after "Zymurgy" (if that were a keyword).

marcowanger · 09-14-2011, 01:27 PM

Thanks Keith, that is why we should (for now) implement a strict requirement for new tag, and when we comes by old tags, convert them to the "standard" format.

krobison · 09-14-2011, 01:27 PM

One other note: I have a backlog of about 50 articles on tools that are not yet in the Wiki. Realistically, it will be a long time before I get that list cleared.

If anyone is interested, I could post batches of links to them here & distribute the load.

marcowanger · 09-14-2011, 01:35 PM

Then post it here. Let's make a google spreadsheet with a column called "Uploaded to Wiki" and "Check by"

Thanks

dan · 09-14-2011, 01:42 PM

Quote:

Originally Posted by krobison

One other note: I have a backlog of about 50 articles on tools that are not yet in the Wiki. Realistically, it will be a long time before I get that list cleared.

If anyone is interested, I could post batches of links to them here & distribute the load.

Please do!

Can you post the list on a page of the wiki? then I can format links to the appropriate pages

Cheers,

dan · 09-14-2011, 01:45 PM

Quote:

Originally Posted by marcowanger

Help make the Wiki awesome!

Awesome!

Quote:

Originally Posted by marcowanger

While you are editing and using the wiki, please also let us know about any issues you have with the wiki software itself -- things perhaps only an administrator can change.

The Wiki Discussion Forum is a good place to discuss issues with the wiki.

The things that only an admin can change should be minimal... wiki is for everyone :-)

james hadfield · 09-16-2011, 01:44 PM

I've been off radar for a while so sorry if the question has already been asked but I wondered why there are no protocols for lab methods on the wiki?

dan · 09-16-2011, 02:29 PM

Quote:

Originally Posted by james hadfield

I've been off radar for a while so sorry if the question has already been asked but I wondered why there are no protocols for lab methods on the wiki?

Wet lab protocols should be covered on OWW, if not, by all means, add a section to build them! (are they currently discussed in the forums?)

Cheers,

ECO · 09-16-2011, 03:15 PM

James, I agree...I have had plans for a long time to do such a thing...just no time. I'd love to derive a series of completely "open source" protocols....

Please feel free to add a structure or specific protocols you feel are important!

usad · 09-18-2011, 06:07 AM

Hi Dan,

how do you calculate the article score? It seems I can massivley boost that by just adding the formalized fields. But I reckon that was the idea, as one can also sort by content size?
Maybe it should also be renamed to Article Score and Article Size or something as not to be confused with software score and size if someone stumbled over the Software wikie site?

Anyway thanks a million time for that, it makes finding articles that need improvement so much easier. (Unfortunately there are so many of them

)

Cheers,
Björn

PS Having a lab howto/protocol section would indeed be great. I like having things in one place.

dan · 09-18-2011, 06:56 AM

Cheers usad, I'm going to reply in a new thread.

Each new topic should get it's own thread: http://producingoss.com/en/communications.html

ETHANol · 09-18-2011, 07:23 AM

This may be a little beyond the scope of this topic and/or the Wiki, but perhaps the addition of a wet-lab protocols section would make the Wiki more complete.

I'm not what the best way to implement this would be but I think in theory it is a good idea.

dan · 09-18-2011, 07:28 AM

Quote:

Originally Posted by ETHANol

This may be a little beyond the scope of this topic and/or the Wiki, but perhaps the addition of a wet-lab protocols section would make the Wiki more complete.

I'm not what the best way to implement this would be but I think in theory it is a good idea.

Yup, sounds like a good idea. I'd guess, one page per protocol, free text protocols with tags for protocol:

* type
* technology
* purpose...

I guess, we should start a new thread to discuss this idea.

marcowanger · 09-18-2011, 07:50 PM

Quote:

Originally Posted by dan

Yup, sounds like a good idea. I'd guess, one page per protocol, free text protocols with tags for protocol:

* type
* technology
* purpose...

I guess, we should start a new thread to discuss this idea.

We have to avoid overlap with openwetware

krobison · 09-21-2011, 08:30 PM

I have a backlog of articles that should probably spawn SeqWiki entries (though in some cases they might mean updating an existing entry) & realistically it will be a while before I can plow through them.

If anyone is interested in tackling some of these, I've created a Google Docs spreadsheet with columns containing some of the information useful for creating an entry & its associated reference and link. It should be editable by anyone -- though this is the first time I've tried this so I won't be surprised if something goes awry. If you enter one, please mark it in the last column with "YES".

dan · 09-22-2011, 12:17 AM

Quote:

Originally Posted by krobison

I have a backlog of articles that should probably spawn SeqWiki entries (though in some cases they might mean updating an existing entry) & realistically it will be a while before I can plow through them.

If anyone is interested in tackling some of these, I've created a Google Docs spreadsheet with columns containing some of the information useful for creating an entry & its associated reference and link. It should be editable by anyone -- though this is the first time I've tried this so I won't be surprised if something goes awry. If you enter one, please mark it in the last column with "YES".

I'll load this into the wiki using the DT extension:
http://www.mediawiki.org/wiki/Extension

ata_Transfer

biblio · 04-13-2012, 11:49 PM

I still can not understand your problem, but the answer given by my friends can help me in solving problems similar to you. soursop and cancer

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09-14-2011, 12:51 PM	#1
marcowanger Senior Member Location: Hong Kong Join Date: Dec 2008 Posts: 350	Let's make the SEQwiki even more awesome Help make the Wiki awesome! The SEQanswers wiki (or "SEQwiki" for short) is a great help for users of this forum: It's a catalog of high-throughput sequencing tools. There is currently an effort to get the SEQanswers forum and the wiki published in the next NAR database issue. This is a great opportunity to get the wiki in shape: Some of the tool descriptions are just "stubs", but in order for those pages to be really helpful, we need just ten minutes of your time. We invite everyone to pick one (or of course more!) tools that she or he uses and improve its description in the wiki. If you are the author of the tool, it is the best time to advertise there by writing concise description to help people choose the RIGHT tools. This will help others tremendously when they decide which tool to use. It's also the perfect opportunity to write down the sometimes annoying things that are often not mentioned on the homepages of those tools. Here are some suggestions what you could write about your tool: Which tasks is the tool good at? (something like: "really fast read mapping") What are the limitations? In which situations would the tool not be appropriate? ("cannot find indels", "needs at least least 32 GB RAM") Are there any pitfalls? Any idiosyncrasies when using the tool? ("be careful: if the input file is corrupt, there's no error message -- and the results will even look meaningful"). Hidden requirement? e.g. that said memory efficient but require 32GB or more for a reasonable small dataset? Which alternative tools exist? ("if you still use MAQ, you should switch to BWA") Are there related tools? (on the BWA page: "Seal uses the BWA algorithm, but runs on a Hadoop cluster") Since the wiki is there to help us decide which tool to use for a specific purpose, please also try to update the tags for your tool. Just try to make it fit into the "Browse software" page! While you are editing and using the wiki, please also let us know about any issues you have with the wiki software itself -- things perhaps only an administrator can change. Do any templates look ugly? Is the navigation too confusing? Don't like the fonts? We cannot promise to take care of everything, but *please tell us*! Writing by M Martin. Thanks! The SeqWiki Publishing team want to thank you for the help __________________ Marco

09-14-2011, 01:08 PM	#2
marcowanger Senior Member Location: Hong Kong Join Date: Dec 2008 Posts: 350	Dear all, in the meantime, please be reminded Bioinformatics method means METHOD employed. Most of the existing tags are fine. Biological domain refers to something bigger. e.g. Genomics, Transcriptomics, Chip-Seq, etc. Please don't tag Alignment* as domains. I am not sure if tag is case-sensitive. If we assume it is not. Please start with the tag with a capital letter. Alignment NOT alignment If the word is two word, please make it two. For example "Method" Base Call, not basecall* Please correct me if the case is case-insensitive Thanks a lot __________________ Marco

09-14-2011, 01:27 PM	#4
marcowanger Senior Member Location: Hong Kong Join Date: Dec 2008 Posts: 350	Thanks Keith, that is why we should (for now) implement a strict requirement for new tag, and when we comes by old tags, convert them to the "standard" format. __________________ Marco

09-14-2011, 01:35 PM	#6
marcowanger Senior Member Location: Hong Kong Join Date: Dec 2008 Posts: 350	Then post it here. Let's make a google spreadsheet with a column called "Uploaded to Wiki" and "Check by" Thanks __________________ Marco

09-14-2011, 01:25 PM	#3
krobison Senior Member Location: Boston area Join Date: Nov 2007 Posts: 747	Tags are case (and punctuation!) sensitive and currently are sorted so that uppercase comes first and lowercase later. So "Assembly Visualization" will be soon followed by "Assembly visualization", but "assembly visualization" will be after "Zymurgy" (if that were a keyword).

09-16-2011, 01:44 PM	#9
james hadfield Moderator Cambridge, UK Community Forum Location: Cambridge, UK Join Date: Feb 2008 Posts: 221	I've been off radar for a while so sorry if the question has already been asked but I wondered why there are no protocols for lab methods on the wiki?

09-16-2011, 03:15 PM	#11
ECO --Site Admin-- Location: SF Bay Area, CA, USA Join Date: Oct 2007 Posts: 1,358	James, I agree...I have had plans for a long time to do such a thing...just no time. I'd love to derive a series of completely "open source" protocols.... Please feel free to add a structure or specific protocols you feel are important!

09-18-2011, 06:07 AM	#12
usad Member Location: aachen Join Date: Sep 2009 Posts: 53	Article score Hi Dan, how do you calculate the article score? It seems I can massivley boost that by just adding the formalized fields. But I reckon that was the idea, as one can also sort by content size? Maybe it should also be renamed to Article Score and Article Size or something as not to be confused with software score and size if someone stumbled over the Software wikie site? Anyway thanks a million time for that, it makes finding articles that need improvement so much easier. (Unfortunately there are so many of them ) Cheers, Björn PS Having a lab howto/protocol section would indeed be great. I like having things in one place.

09-18-2011, 06:56 AM	#13
dan wiki wiki Location: Cambridge, England Join Date: Jul 2008 Posts: 266	Cheers usad, I'm going to reply in a new thread. Each new topic should get it's own thread: http://producingoss.com/en/communications.html __________________ Homepage: Dan Bolser MetaBase the database of biological databases.

09-18-2011, 07:23 AM	#14
ETHANol Senior Member Location: Western Australia Join Date: Feb 2010 Posts: 308	This may be a little beyond the scope of this topic and/or the Wiki, but perhaps the addition of a wet-lab protocols section would make the Wiki more complete. I'm not what the best way to implement this would be but I think in theory it is a good idea. __________________ -------------- Ethan

09-21-2011, 08:30 PM	#17
krobison Senior Member Location: Boston area Join Date: Nov 2007 Posts: 747	I have a backlog of articles that should probably spawn SeqWiki entries (though in some cases they might mean updating an existing entry) & realistically it will be a while before I can plow through them. If anyone is interested in tackling some of these, I've created a Google Docs spreadsheet with columns containing some of the information useful for creating an entry & its associated reference and link. It should be editable by anyone -- though this is the first time I've tried this so I won't be surprised if something goes awry. If you enter one, please mark it in the last column with "YES".

04-13-2012, 11:49 PM	#19
biblio Junior Member Location: london Join Date: Apr 2012 Posts: 2	I still can not understand your problem, but the answer given by my friends can help me in solving problems similar to you. soursop and cancer Last edited by biblio; 07-27-2012 at 09:25 PM.