New Applications Forums

ECO · 11-19-2008, 12:41 PM

In an effort to increase the organization of the discussions and make things easier to find...I've created a new set of "Applications" forums:

Library Generation

Epigenetics

RNA Sequencing

De novo discovery

My intent is to segment the purely scientific/biology discussions away from the previously instrument provider-focused areas. I think this organization offers more opportunity for people with different instruments to cross-pollinate, as regardless of what chemistry/instrument produces the data, the biology remains (roughly!) the same.

I welcome comments, suggestions, mocking, laughing, whatever!

ECO · 11-19-2008, 02:47 PM

Just added Genomic Resequencing

jOn · 11-20-2008, 03:10 AM

Well done ECO, I can see this being of particular benefit to people new to NextGen sequencing that probably don’t own a machine but are interested in applying for grants etc; it will definitely improve accessibility to the site. I was wondering what you or anyone else thought about including a “metagenomics” section and (the application of most interest to me) a “molecular diagnostics” section.

Further to this – in the “about me” section we can define ourselves by “location” and “instrument”, would it be useful for members to be able to define themselves also by “specialism/field/interest” e.g. bioinformatics or epigenetics? Just a thought.

ECO · 11-20-2008, 05:59 AM

Thanks jOn...good thoughts. I will definitely work towards the new forums you mentioned.

I've been toying with a few ideas on how to improve the user profiles. Most specifically reducing the emphasis on "what instrument do you have". I don't think I want to restrict the field of interests to a list or menu (because I don't know all of the possibilities, and if I did it would be an immense list), so I'd have to open it up to being a user filled area.

Good thoughts, keep 'em coming.

RudyS · 01-14-2009, 07:32 AM

Eco

Is there a separate forum for sequence Annotation? anybody have suggestions for (microbial) genome annotation tools to use after assembling contigs/genomes?

Thanks

RudyS

bioinfosm · 01-14-2009, 07:49 AM

Quote:

Originally Posted by RudyS

Eco

Is there a separate forum for sequence Annotation? anybody have suggestions for (microbial) genome annotation tools to use after assembling contigs/genomes?

Thanks

RudyS

I am looking for one too.. Rudy, please pass along in case you stumble on something

ECO · 01-14-2009, 05:30 PM

Quote:

Originally Posted by RudyS

Eco

Is there a separate forum for sequence Annotation? anybody have suggestions for (microbial) genome annotation tools to use after assembling contigs/genomes?

Thanks

RudyS

Quote:

Originally Posted by bioinfosm

I am looking for one too.. Rudy, please pass along in case you stumble on something

Hey guys,

I'm happy to create such a forum if there is enough interest...is this not something that could belong in the bioinformatics forum? Maybe it's time to think about subdividing that forum? I'm not eager to do that as it forces casual browsers to visit many smaller forums...but it's worth discussing....

RudyS · 01-15-2009, 08:28 AM

ECO

i dont see much "bio" in the bioinformatics forum ... mostly still questions about how to assemble DNA ... i did see a post from bioinfosm from almost a year ago!
1/17/08
"Just wanted to initiate some bioinfo discussions ... makes up a major chunk of this high throughput sequencing effort .. after getting the sequence
Any members here having experience with the data .. using it with some open access or in-house tools for mutation analysis, etc."

sooo it looks like two separate groups of problems ... maybe the people doing the annotation are biologists? i have found B2G useful
http://www.blast2go.org/home
but wonder how other people deal with large annotation problems ... actually my problem is relatively small ... 5 MBase microbial genome

RudyS

RudyS · 01-15-2009, 08:29 AM

ECO

i dont see much "bio" in the bioinformatics forum ... mostly still questions about how to assemble DNA ... i did see a post from bioinfosm from almost a year ago!
1/17/08
"Just wanted to initiate some bioinfo discussions ... makes up a major chunk of this high throughput sequencing effort .. after getting the sequence
Any members here having experience with the data .. using it with some open access or in-house tools for mutation analysis, etc."

sooo it looks like two separate groups of problems ... maybe the people doing the annotation are biologists? i have found B2G useful
http://www.blast2go.org/home
but wonder how other people deal with large annotation problems ... actually my problem is relatively small ... 5 MBase microbial genome

RudyS

Stegger · 03-04-2009, 01:13 AM

Quote:

Originally Posted by bioinfosm

I am looking for one too.. Rudy, please pass along in case you stumble on something

I agree, would be great to have a talk about sequence annotation!

I will make a thread here as ECO suggested http://seqanswers.com/forums/showthr...=3854#post3854

Stegger

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11-19-2008, 12:41 PM	#1
ECO --Site Admin-- Location: SF Bay Area, CA, USA Join Date: Oct 2007 Posts: 1,358	New Applications Forums In an effort to increase the organization of the discussions and make things easier to find...I've created a new set of "Applications" forums: Library Generation Epigenetics RNA Sequencing De novo discovery My intent is to segment the purely scientific/biology discussions away from the previously instrument provider-focused areas. I think this organization offers more opportunity for people with different instruments to cross-pollinate, as regardless of what chemistry/instrument produces the data, the biology remains (roughly!) the same. I welcome comments, suggestions, mocking, laughing, whatever!

11-19-2008, 02:47 PM	#2
ECO --Site Admin-- Location: SF Bay Area, CA, USA Join Date: Oct 2007 Posts: 1,358	Just added Genomic Resequencing

11-20-2008, 03:10 AM	#3
jOn Member Location: UK Join Date: Oct 2008 Posts: 19	Well done ECO, I can see this being of particular benefit to people new to NextGen sequencing that probably don’t own a machine but are interested in applying for grants etc; it will definitely improve accessibility to the site. I was wondering what you or anyone else thought about including a “metagenomics” section and (the application of most interest to me) a “molecular diagnostics” section. Further to this – in the “about me” section we can define ourselves by “location” and “instrument”, would it be useful for members to be able to define themselves also by “specialism/field/interest” e.g. bioinformatics or epigenetics? Just a thought.

11-20-2008, 05:59 AM	#4
ECO --Site Admin-- Location: SF Bay Area, CA, USA Join Date: Oct 2007 Posts: 1,358	Thanks jOn...good thoughts. I will definitely work towards the new forums you mentioned. I've been toying with a few ideas on how to improve the user profiles. Most specifically reducing the emphasis on "what instrument do you have". I don't think I want to restrict the field of interests to a list or menu (because I don't know all of the possibilities, and if I did it would be an immense list), so I'd have to open it up to being a user filled area. Good thoughts, keep 'em coming.

01-14-2009, 07:32 AM	#5
RudyS Member Location: new york Join Date: May 2008 Posts: 20	Eco Is there a separate forum for sequence Annotation? anybody have suggestions for (microbial) genome annotation tools to use after assembling contigs/genomes? Thanks RudyS

01-15-2009, 08:28 AM	#8
RudyS Member Location: new york Join Date: May 2008 Posts: 20	ECO i dont see much "bio" in the bioinformatics forum ... mostly still questions about how to assemble DNA ... i did see a post from bioinfosm from almost a year ago! 1/17/08 "Just wanted to initiate some bioinfo discussions ... makes up a major chunk of this high throughput sequencing effort .. after getting the sequence Any members here having experience with the data .. using it with some open access or in-house tools for mutation analysis, etc." sooo it looks like two separate groups of problems ... maybe the people doing the annotation are biologists? i have found B2G useful http://www.blast2go.org/home but wonder how other people deal with large annotation problems ... actually my problem is relatively small ... 5 MBase microbial genome RudyS

01-15-2009, 08:29 AM	#9
RudyS Member Location: new york Join Date: May 2008 Posts: 20	ECO i dont see much "bio" in the bioinformatics forum ... mostly still questions about how to assemble DNA ... i did see a post from bioinfosm from almost a year ago! 1/17/08 "Just wanted to initiate some bioinfo discussions ... makes up a major chunk of this high throughput sequencing effort .. after getting the sequence Any members here having experience with the data .. using it with some open access or in-house tools for mutation analysis, etc." sooo it looks like two separate groups of problems ... maybe the people doing the annotation are biologists? i have found B2G useful http://www.blast2go.org/home but wonder how other people deal with large annotation problems ... actually my problem is relatively small ... 5 MBase microbial genome RudyS