Anyone using Mimosa?

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Anyone using Mimosa?

Scott Cain
Hi All,

I'm wondering if anybody is using Mimosa, a project started a few years ago to provide a flexible web interface for sequence similarity searching tools like BLAST (https://github.com/GMOD/mimosa).  I'm looking for something very much along these lines but I realize Mimosa has been quiescent since the developers working on it have left.  I wouldn't mind seeing it resurrected but I also don't have a huge amount of time to put into it either.

Thanks,
Scott


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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Anyone using Mimosa?

Fields, Christopher J
Sounds cool, but there are a ton of issues filed for it, mainly from a few users/devs (Duke Leto is one of them and he’s not really involved on GMOD-related work anymore).  

My only concern is how much of this effort replicates what Galaxy does.  Or is the emphasis on the ease of installation and setup?

chris

On Jul 15, 2015, at 8:53 AM, Scott Cain <[hidden email]> wrote:

Hi All,

I'm wondering if anybody is using Mimosa, a project started a few years ago to provide a flexible web interface for sequence similarity searching tools like BLAST (https://github.com/GMOD/mimosa).  I'm looking for something very much along these lines but I realize Mimosa has been quiescent since the developers working on it have left.  I wouldn't mind seeing it resurrected but I also don't have a huge amount of time to put into it either.

Thanks,
Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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Re: Anyone using Mimosa?

Scott Cain
Hi Chris,

Galaxy is an outstanding tool, but the point of Mimosa is to have a tool that easily integrates into a MOD website to allow users to blast/blat their sequences easily and have those results tie back into the website.  I don't think Galaxy fits that bill.

Scott


On Wed, Jul 15, 2015 at 10:18 AM, Fields, Christopher J <[hidden email]> wrote:
Sounds cool, but there are a ton of issues filed for it, mainly from a few users/devs (Duke Leto is one of them and he’s not really involved on GMOD-related work anymore).  

My only concern is how much of this effort replicates what Galaxy does.  Or is the emphasis on the ease of installation and setup?

chris

On Jul 15, 2015, at 8:53 AM, Scott Cain <[hidden email]> wrote:

Hi All,

I'm wondering if anybody is using Mimosa, a project started a few years ago to provide a flexible web interface for sequence similarity searching tools like BLAST (https://github.com/GMOD/mimosa).  I'm looking for something very much along these lines but I realize Mimosa has been quiescent since the developers working on it have left.  I wouldn't mind seeing it resurrected but I also don't have a huge amount of time to put into it either.

Thanks,
Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Anyone using Mimosa?

Fields, Christopher J
Ok, so a focus on ease of use and installation makes sense (as well as possibly packaging it up with other GMOD tools ala GMOD in the Cloud, maybe).  We just had someone ask for a very similar thing locally.

Then, as you already mentioned, it really depends who can take it on.

chris

On Jul 15, 2015, at 10:02 AM, Scott Cain <[hidden email]> wrote:

Hi Chris,

Galaxy is an outstanding tool, but the point of Mimosa is to have a tool that easily integrates into a MOD website to allow users to blast/blat their sequences easily and have those results tie back into the website.  I don't think Galaxy fits that bill.

Scott


On Wed, Jul 15, 2015 at 10:18 AM, Fields, Christopher J <[hidden email]> wrote:
Sounds cool, but there are a ton of issues filed for it, mainly from a few users/devs (Duke Leto is one of them and he’s not really involved on GMOD-related work anymore).  

My only concern is how much of this effort replicates what Galaxy does.  Or is the emphasis on the ease of installation and setup?

chris

On Jul 15, 2015, at 8:53 AM, Scott Cain <[hidden email]> wrote:

Hi All,

I'm wondering if anybody is using Mimosa, a project started a few years ago to provide a flexible web interface for sequence similarity searching tools like BLAST (https://github.com/GMOD/mimosa).  I'm looking for something very much along these lines but I realize Mimosa has been quiescent since the developers working on it have left.  I wouldn't mind seeing it resurrected but I also don't have a huge amount of time to put into it either.

Thanks,
Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="&#43;12163923087" target="_blank" class="">216-392-3087
Ontario Institute for Cancer Research
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


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Re: Anyone using Mimosa?

Peter Cock
In reply to this post by Scott Cain
Hi Scott,

From your original email I was going to suggest something like
http://www.sequenceserver.com/ but you've clarified you want
a BLAST interface within a GMOD website?

Peter

P.S. I have a conflict of interest in promoting BLAST+ in Galaxy
http://dx.doi.org/10.1101/014043

On Wed, Jul 15, 2015 at 4:02 PM, Scott Cain <[hidden email]> wrote:

> Hi Chris,
>
> Galaxy is an outstanding tool, but the point of Mimosa is to have a tool
> that easily integrates into a MOD website to allow users to blast/blat their
> sequences easily and have those results tie back into the website.  I don't
> think Galaxy fits that bill.
>
> Scott
>
>
> On Wed, Jul 15, 2015 at 10:18 AM, Fields, Christopher J
> <[hidden email]> wrote:
>>
>> Sounds cool, but there are a ton of issues filed for it, mainly from a few
>> users/devs (Duke Leto is one of them and he’s not really involved on
>> GMOD-related work anymore).
>>
>> My only concern is how much of this effort replicates what Galaxy does.
>> Or is the emphasis on the ease of installation and setup?
>>
>> chris
>>
>> On Jul 15, 2015, at 8:53 AM, Scott Cain <[hidden email]> wrote:
>>
>> Hi All,
>>
>> I'm wondering if anybody is using Mimosa, a project started a few years
>> ago to provide a flexible web interface for sequence similarity searching
>> tools like BLAST (https://github.com/GMOD/mimosa).  I'm looking for
>> something very much along these lines but I realize Mimosa has been
>> quiescent since the developers working on it have left.  I wouldn't mind
>> seeing it resurrected but I also don't have a huge amount of time to put
>> into it either.
>>
>> Thanks,
>> Scott
>>
>>

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Re: Anyone using Mimosa?

Scott Cain
Hi Peter,

Actually, I want it for use in WormBase, so it's not exactly a GMOD website (that is, it doesn't use Tripal--I just sent it to the Tripal website to have a reasonably large audience, and since Tripal people are interested in web development, it seemed reasonable).  I'll take a look at SequenceServer.

Thanks,
Scott


On Wed, Jul 15, 2015 at 11:21 AM, Peter Cock <[hidden email]> wrote:
Hi Scott,

>From your original email I was going to suggest something like
http://www.sequenceserver.com/ but you've clarified you want
a BLAST interface within a GMOD website?

Peter

P.S. I have a conflict of interest in promoting BLAST+ in Galaxy
http://dx.doi.org/10.1101/014043

On Wed, Jul 15, 2015 at 4:02 PM, Scott Cain <[hidden email]> wrote:
> Hi Chris,
>
> Galaxy is an outstanding tool, but the point of Mimosa is to have a tool
> that easily integrates into a MOD website to allow users to blast/blat their
> sequences easily and have those results tie back into the website.  I don't
> think Galaxy fits that bill.
>
> Scott
>
>
> On Wed, Jul 15, 2015 at 10:18 AM, Fields, Christopher J
> <[hidden email]> wrote:
>>
>> Sounds cool, but there are a ton of issues filed for it, mainly from a few
>> users/devs (Duke Leto is one of them and he’s not really involved on
>> GMOD-related work anymore).
>>
>> My only concern is how much of this effort replicates what Galaxy does.
>> Or is the emphasis on the ease of installation and setup?
>>
>> chris
>>
>> On Jul 15, 2015, at 8:53 AM, Scott Cain <[hidden email]> wrote:
>>
>> Hi All,
>>
>> I'm wondering if anybody is using Mimosa, a project started a few years
>> ago to provide a flexible web interface for sequence similarity searching
>> tools like BLAST (https://github.com/GMOD/mimosa).  I'm looking for
>> something very much along these lines but I realize Mimosa has been
>> quiescent since the developers working on it have left.  I wouldn't mind
>> seeing it resurrected but I also don't have a huge amount of time to put
>> into it either.
>>
>> Thanks,
>> Scott
>>
>>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: [Gmod-tripal-devel] Anyone using Mimosa?

Chris Childers
Hi Scott,

I've seen a few groups that use Sequence server, and it seemed pretty straightforward to stand up and customize.

Another alternative is the BLAST application we are using, developed in Django. This runs in parallel to our Tripal and annotation resources.
https://i5k.nal.usda.gov/webapp/blast/
The source is available up on github if you are interested in checking it out.

Chris


On Wed, Jul 15, 2015 at 11:32 AM, Scott Cain <[hidden email]> wrote:
Hi Peter,

Actually, I want it for use in WormBase, so it's not exactly a GMOD website (that is, it doesn't use Tripal--I just sent it to the Tripal website to have a reasonably large audience, and since Tripal people are interested in web development, it seemed reasonable).  I'll take a look at SequenceServer.

Thanks,
Scott


On Wed, Jul 15, 2015 at 11:21 AM, Peter Cock <[hidden email]> wrote:
Hi Scott,

>From your original email I was going to suggest something like
http://www.sequenceserver.com/ but you've clarified you want
a BLAST interface within a GMOD website?

Peter

P.S. I have a conflict of interest in promoting BLAST+ in Galaxy
http://dx.doi.org/10.1101/014043


On Wed, Jul 15, 2015 at 4:02 PM, Scott Cain <[hidden email]> wrote:
> Hi Chris,
>
> Galaxy is an outstanding tool, but the point of Mimosa is to have a tool
> that easily integrates into a MOD website to allow users to blast/blat their
> sequences easily and have those results tie back into the website.  I don't
> think Galaxy fits that bill.
>
> Scott
>
>
> On Wed, Jul 15, 2015 at 10:18 AM, Fields, Christopher J
> <[hidden email]> wrote:
>>
>> Sounds cool, but there are a ton of issues filed for it, mainly from a few
>> users/devs (Duke Leto is one of them and he’s not really involved on
>> GMOD-related work anymore).
>>
>> My only concern is how much of this effort replicates what Galaxy does.
>> Or is the emphasis on the ease of installation and setup?
>>
>> chris
>>
>> On Jul 15, 2015, at 8:53 AM, Scott Cain <[hidden email]> wrote:
>>
>> Hi All,
>>
>> I'm wondering if anybody is using Mimosa, a project started a few years
>> ago to provide a flexible web interface for sequence similarity searching
>> tools like BLAST (https://github.com/GMOD/mimosa).  I'm looking for
>> something very much along these lines but I realize Mimosa has been
>> quiescent since the developers working on it have left.  I wouldn't mind
>> seeing it resurrected but I also don't have a huge amount of time to put
>> into it either.
>>
>> Thanks,
>> Scott
>>
>>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

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