simplifying Galaxy interface to the max (zen-like)
Dear Galaxy-Devs, I am developing a tool for biologists, I managed to integrate it with Galaxy (it's a KNIME/R-based machine learning workflow). This tool doesn't require a lot of interaction from the user - just a list of IDs pasted-in and maybe 1-2 text entry fields - then it's just Execute. Even though the inner works of Galaxy are great and I got a grip of it, we believe that for our needs the workflow-based system with a tool and data list is a bit confusing for non-computational people who don't want to spend too much time on learning the interface (I know it's not complicated, but we know how people are...). So what we're aiming for is to put some sort of Google Search-like front, as simple as possible. Could anyone point me in the right direction, how to do it ? Or maybe anyone ever did something like this ? I could imagine that it should be easy, since we want to remove almost all elements, not write them from scratch. Any ideas ? Best, Piotr
Hi Piotr, I see two basic approaches: * You can use an API to interact with any Galaxy so writing a single webapp that does just that is an option. However you would need to interact with user's credentials as API would need a user key for most of the interactions. You can use e.g. BioBlend library if you want to use the API in Python. * If you have your own Galaxy you can customize the frontend directly in its codebase, however I would not recommend this as every future Galaxy update will probably cause merge problems resulting in your Galaxy to be out of date. Thank you for using Galaxy. Martin On Mon, Sep 14, 2015 at 11:37 AM Piotr Grabowski <kajocina@gmail.com> wrote:
Dear Galaxy-Devs,
I am developing a tool for biologists, I managed to integrate it with Galaxy (it's a KNIME/R-based machine learning workflow). This tool doesn't require a lot of interaction from the user - just a list of IDs pasted-in and maybe 1-2 text entry fields - then it's just Execute.
Even though the inner works of Galaxy are great and I got a grip of it, we believe that for our needs the workflow-based system with a tool and data list is a bit confusing for non-computational people who don't want to spend too much time on learning the interface (I know it's not complicated, but we know how people are...).
So what we're aiming for is to put some sort of Google Search-like front, as simple as possible. Could anyone point me in the right direction, how to do it ? Or maybe anyone ever did something like this ? I could imagine that it should be easy, since we want to remove almost all elements, not write them from scratch.
Any ideas ?
Best, Piotr ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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I don't have a ton of advice here, I imagine you could hack up Galaxy to do it. If you a have a fixed workflow or fixed collections of workflows and very clear vision of what the interface should be I guess I would just create a web app and target the Galaxy API. Two projects to checkout would be refinery - which is a webapp that does a lot of stuff including driving Galaxy workflows. It is a bit more stripped down than Galaxy and may emphasize what you want: https://github.com/parklab/refinery-platform A good example of actually modifying Galaxy to emphasize certain workflows would be RNA Rocket (http://rnaseq.pathogenportal.org/). Checkout out their paper here - http://bioinformatics.oxfordjournals.org/content/early/2015/02/02/bioinforma.... -John On Mon, Sep 14, 2015 at 4:37 PM, Piotr Grabowski <kajocina@gmail.com> wrote:
Dear Galaxy-Devs,
I am developing a tool for biologists, I managed to integrate it with Galaxy (it's a KNIME/R-based machine learning workflow). This tool doesn't require a lot of interaction from the user - just a list of IDs pasted-in and maybe 1-2 text entry fields - then it's just Execute.
Even though the inner works of Galaxy are great and I got a grip of it, we believe that for our needs the workflow-based system with a tool and data list is a bit confusing for non-computational people who don't want to spend too much time on learning the interface (I know it's not complicated, but we know how people are...).
So what we're aiming for is to put some sort of Google Search-like front, as simple as possible. Could anyone point me in the right direction, how to do it ? Or maybe anyone ever did something like this ? I could imagine that it should be easy, since we want to remove almost all elements, not write them from scratch.
Any ideas ?
Best, Piotr
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Thank you for your advice, I think we will go for writing our own web app that will use the Galaxy API as this seems the most flexible solution for the future (having the potential Galaxy updates in mind). Best regards, Piotr On Mon, Sep 14, 2015 at 5:46 PM, John Chilton <jmchilton@gmail.com> wrote:
I don't have a ton of advice here, I imagine you could hack up Galaxy to do it. If you a have a fixed workflow or fixed collections of workflows and very clear vision of what the interface should be I guess I would just create a web app and target the Galaxy API.
Two projects to checkout would be refinery - which is a webapp that does a lot of stuff including driving Galaxy workflows. It is a bit more stripped down than Galaxy and may emphasize what you want:
https://github.com/parklab/refinery-platform
A good example of actually modifying Galaxy to emphasize certain workflows would be RNA Rocket (http://rnaseq.pathogenportal.org/). Checkout out their paper here -
http://bioinformatics.oxfordjournals.org/content/early/2015/02/02/bioinforma... .
-John
Dear Galaxy-Devs,
I am developing a tool for biologists, I managed to integrate it with Galaxy (it's a KNIME/R-based machine learning workflow). This tool doesn't require a lot of interaction from the user - just a
of IDs pasted-in and maybe 1-2 text entry fields - then it's just Execute.
Even though the inner works of Galaxy are great and I got a grip of it, we believe that for our needs the workflow-based system with a tool and data list is a bit confusing for non-computational people who don't want to spend too much time on learning the interface (I know it's not complicated, but we know how people are...).
So what we're aiming for is to put some sort of Google Search-like front, as simple as possible. Could anyone point me in the right direction, how to do it ? Or maybe anyone ever did something like this ? I could imagine that it should be easy, since we want to remove almost all elements, not write
On Mon, Sep 14, 2015 at 4:37 PM, Piotr Grabowski <kajocina@gmail.com> wrote: list them
from scratch.
Any ideas ?
Best, Piotr
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (3)
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John Chilton -
Martin Čech -
Piotr Grabowski