Fwd: Development tracking, communication and high-level summary for OpenSWATH.

[Pratik Jagtap]

OpenSWATH in GalaxyP Tracking.

---------- Forwarded message ----------
From: Sarah Parker <spar...@gmail.com>
Date: Fri, Feb 13, 2015 at 8:59 PM
Subject: Re: Development tracking, communication and high-level summary for OpenSWATH.
To: Pratik Jagtap <pja...@umn.edu>
Cc: Björn Grüning <bjoern....@gmail.com>, Ira Cooke <irac...@gmail.com>

Hello all, 

This sounds like a good approach.

I agree, lets make sure openSWATH is working first (and I think it will be fast given Bjorn's progress already) - then tackle the library steps.

Looking forward to starting to test these components!

Thanks!

Sarah

On Feb 13, 2015, at 8:40 PM, Pratik Jagtap wrote:

Hello Bjoern, Ira and Sarah,

Please how this plan looks -

A) For developmental tracking - we use Github as we are doing right now.

B) For communication - "wrapping done", "tool installed" and "testing" - we can use email and copy to gal...@umn.edu (like I have done for this mail) so that we can keep track of communication.

C) For high-level summary of three major steps (Wrap, Install and Test) - we can use github as Bjoern has suggested. I can also perform a weekly update of the powerpoint slide that I had shared earlier - so that we can prioritize tasks.

Let me know if we are on the same page so that we can get started on this exciting project.

We discussed this at the GalaxyP weekly meeting and Tim mentioned that let us prioritize getting the OpenSWATH workflow running first.

Regards,

Pratik

Pratik Jagtap,

Managing Director, Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN 55108      

Phone: 612-624-9275

http://z.umn.edu/multiomicsnbt

On Wed, Feb 11, 2015 at 1:01 PM, Björn Grüning <bjoern....@gmail.com> wrote:

Hi,

> Yes, I actually asked Pratik for this kind of monitoring -
>
> Since we have so many people working from locations all over the world (so awesome!), I know I personally find it difficult to know where various components are at and what is needed next.

So true. This is also the reason I would try to not use yet another
sheet of information.
The Galaxy team is using github/bitbucket and Trello and it has served
them well.

> I think the GitHub is a great place to track and communicate the wrapping of all the components,
> but ultimately it would be good to have a page with very high-level summary of the status of the three major steps (Wrap, Install, Test) for th main modules we are working to generate.

We could have a overall github issue that is tracking all other tools.

> As more of an 'informed user' than a programmer I can get lost in the Git Hub threads, so something more dummy proof for my sake would be really helpful.
> The teams working on wrapping the various components can decide collectively when they are ready to mark that module as 'complete',
> then Trevor (or other designated person) can start the install onto GalaxyP, mark that as complete when he's done it, and myself or another user can test the functionality.
> I can check in on the summary page to see what's ready for transition to the next step and do my part as needed.

Got it. Maybe I'm thinking to developer oriented :)

> The trello page might be a simple enough solution. In my mind a simple color code for the tabs would be so easy: red = some hurdle that needs to be resolved, yellow = in progress, green = finished and ready for the next step

Don't know if Trello can color code the lists, but we could have a list
with "to be wrapped", "to be tested", "to be installed"  and so on.
Everyone can subscribe to every card that he/she is interested.

> Please let me know your thoughts, you guys have done this before and will best know how you like to organize!

I would follow the main Galaxy project. This is fire proofed and most of
us are already used to it, I would guess.

Thanks,
Bjoern

> Thank you,
>
> Sarah
>
>
>
> On Feb 11, 2015, at 11:35 AM, Pratik Jagtap wrote:
>
>> Hello Bjoern,
>>
>> We can use github for tracking developmental work. I am just curious on how we will communicate that the tool has been wrapped and available for installation and later for testing. Through the galaxyp user forum?
>>
>> I think having an overview (like the powerpoint slide) that is updated regularly on the progress will also be good.
>>
>> Inputs from Sarah and Ira (once he returns) would be great -
>>
>> Cheers,
>>
>> Pratik
>>
>> Pratik Jagtap,
>> Managing Director, Center for Mass Spectrometry and Proteomics,
>> 43 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN 55108
>> Phone: 612-624-9275
>> http://z.umn.edu/multiomicsnbt
>>
>> On Wed, Feb 11, 2015 at 1:12 AM, Björn Grüning <bjoern....@gmail.com> wrote:
>> Hi Pratik,
>>
>> Am 11.02.2015 um 04:08 schrieb Pratik Jagtap:
>>> Hello Bjoern,
>>>
>>> Sorry for the late response.
>>>
>>> Sarah and myself discussed about the plans for OpenSWATH in Galaxy. We were
>>> wondering if there is a project tracking board / tool/ website that can
>>> track tools, tasks (wrap, install and test) and teams like the way shown in
>>> attached slide? If we can have a website like a scorecard - we can track
>>> the progress of the project and distribute tasks accordingly. Any ideas?
>>
>> We had a trello board for this:
>>
>> https://trello.com/b/vEfiz617/proteomics
>>
>> But I think we agreed to track everything like this on github as issues.
>> If you feel strong about this and want to use trello we can open it again.
>>
>> Cheers,
>> Bjoern
>>
>>> Regards,
>>>
>>> Pratik
>>>
>>> Pratik Jagtap,
>>> Managing Director, Center for Mass Spectrometry and Proteomics,
>>> 43 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN 55108
>>> Phone: 612-624-9275
>>> *http://z.umn.edu/multiomicsnbt <http://z.umn.edu/multiomicsnbt>*
>>>
>>> On Sat, Feb 7, 2015 at 1:33 AM, Björn Grüning <bjoern....@gmail.com>
>>> wrote:
>>>
>>>> Hi Ira and Pratik,
>>>>
>>>> thanks for working and submitting the poster!
>>>> I have started working on the OpenSwath wrappers in this branch.
>>>>
>>>> https://github.com/galaxyproteomics/tools-galaxyp/tree/msproteomicstools
>>>>
>>>> Cheers,
>>>> Bjoern
>>>>
>>>
>>
>
>

[Pratik Jagtap]

Hello Ira,

Any thoughts on this plan?

Regards,

Pratik

Pratik Jagtap,

Managing Director, Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN 55108      

Phone: 612-624-9275

http://z.umn.edu/multiomicsnbt

[Ira Cooke]

Hi Pratik, 

This seems good to me.  I’m certainly in favour of using github issues for the development side .. but since github issues tend to be very specific and low-level it would also be good to track overall progress towards getting the workflow going.  

Tracking overall progress seems like a task best suited to somebody who will actually run the final workflow (eg Sarah and yourself).  Perhaps an idea would be if you could post a screenshot of your current workflow (ie the bits that work) pointing out what needs to happen next?

Cheers

Ira

[Ira Cooke]

Hi All, 

One further thought … maybe the github wiki is a good place to track progress on implementing the overall openSWATH workflow.

https://github.com/galaxyproteomics/tools-galaxyp/wiki

The wiki can be edited in the browser and supports screenshots/code snippets etc.

I suggest creating a wiki page called “OpenSWATH”.  During development it can include progress, and as we complete sections we can convert that into user documentation.

How does that sound?

Cheers

Ira

On 16 Feb 2015, at 1:18 pm, Pratik Jagtap <pja...@umn.edu> wrote:

[Pratik Jagtap]

Hello Ira,

Thanks and good inputs.

> Tracking overall progress seems like a task best suited to somebody who will actually run the final workflow (eg Sarah and 

> yourself).  Perhaps an idea would be if you could post a screenshot of your current workflow (ie the bits that work) pointing out > what needs to happen next?

Yes I agree - I will follow upon the overview and progress while coordinating with Sarah and rest.

> github wiki is a good place to track progress on implementing the overall openSWATH workflow.

> https://github.com/galaxyproteomics/tools-galaxyp/wiki

> The wiki can be edited in the browser and supports screenshots/code snippets etc.

I will start a Wiki there and have the current screenshot placed there.

> I suggest creating a wiki page called “OpenSWATH”.  During development it can include progress, and as we complete 

> sections we can convert that into user documentation. How does that sound?

Sounds like a great idea ! We can also use the same for PeptideShaker project?

Thanks and Regards,

Pratik

How does that sound?

Pratik Jagtap,

Managing Director, Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN 55108      

Phone: 612-624-9275

http://z.umn.edu/multiomicsnbt

On Sun, Feb 15, 2015 at 8:32 PM, Ira Cooke <irac...@gmail.com> wrote:

Hi All, 

One further thought … maybe the github wiki is a good place to track progress on implementing the overall openSWATH workflow.

https://github.com/galaxyproteomics/tools-galaxyp/wiki

The wiki can be edited in the browser and supports screenshots/code snippets etc.

I suggest creating a wiki page called “OpenSWATH”.  During development it can include progress, and as we complete sections we can convert that into user documentation.

How does that sound?

Cheers

Ira

On Sun, Feb 15, 2015 at 8:25 PM, Ira Cooke <irac...@gmail.com> wrote:

Hi Pratik, 

This seems good to me.  I’m certainly in favour of using github issues for the development side .. but since github issues tend to be very specific and low-level it would also be good to track overall progress towards getting the workflow going.  

Tracking overall progress seems like a task best suited to somebody who will actually run the final workflow (eg Sarah and yourself).  Perhaps an idea would be if you could post a screenshot of your current workflow (ie the bits that work) pointing out what needs to happen next?

Cheers

Ira

[Pratik Jagtap]

Hello Everyone,

Here is a Wiki that we will use to track and document the progress.

https://github.com/galaxyproteomics/tools-galaxyp/wiki/OpenSWATH-in-Galaxy

I will also follow up on updating a powerpoint slide so that I can use it for screenshot and also to update during GalaxyP meetings.

Regards,

Pratik

Pratik Jagtap,

Managing Director, Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN 55108      

Phone: 612-624-9275

http://z.umn.edu/multiomicsnbt