From ferri.fc at gmail.com Mon Jan 3 05:39:40 2022 From: ferri.fc at gmail.com (=?UTF-8?Q?Ferran_F=C3=A0bregas?=) Date: Mon, 3 Jan 2022 11:39:40 +0100 Subject: [Biopython] Bioinformatics master's degree final project Message-ID: Hi! My name is Ferran F?bregas and I'm working on my bioinformatics master?s degree final project. I?m a computer scientist and a Python veteran but a BioPython newbie. I am writing this email because I would like to dedicate the final project of my master's degree in bioinformatics to the development of a library to implement gene annotation, pathway enrichment and access to gene ontologies from Python, similar to how it can be done in R using functions like enrichPathway from ReactomePA or enrichGo from ClusterProfiler. Have any tools been previously developed to do this using BioPython? Are there any packages similar to Bioconductor's OrgDb, ReactomePA , GOSeq or ClusterProfiler? I?m also working on a BioPython GUI based on PySide6. I've seen some old projects related to BioPython GUI development but seem to be discontinued. I would be very happy to use my time to contribute to the bioPython project, and I?m open to any suggestions or ideas. Thanks in advance, Ferran F?bregas -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephane.teletchea at univ-nantes.fr Mon Jan 3 05:49:00 2022 From: stephane.teletchea at univ-nantes.fr (=?UTF-8?B?VMOpbGV0Y2jDqWEgU3TDqXBoYW5l?=) Date: Mon, 3 Jan 2022 11:49:00 +0100 Subject: [Biopython] Bioinformatics master's degree final project In-Reply-To: References: Message-ID: An HTML attachment was scrubbed... URL: From alexeymorozov1991 at gmail.com Mon Jan 3 06:45:45 2022 From: alexeymorozov1991 at gmail.com (Alexey Morozov) Date: Mon, 3 Jan 2022 19:45:45 +0800 Subject: [Biopython] Bioinformatics master's degree final project In-Reply-To: References: Message-ID: Dear Ferran, There is a Python library for GO enrichment called goenrich ( https://github.com/jdrudolph/goenrich). I haven't used it for the last couple of years, but it did its job in 2018 or so (despite lacking some tests available in eg topGO). OTOH, goenrich repo shows that the last commit was in summer 2020, so maybe they've added something. Back when I used it, BioPython integration was basically absent, they just used their own objects for everything. There is also a library called goatools ( https://github.com/tanghaibao/goatools), but I haven't actually used it, so no comments. ??, 3 ???. 2022 ?. ? 18:40, Ferran F?bregas : > Hi! My name is Ferran F?bregas and I'm working on my bioinformatics > master?s degree final project. I?m a computer scientist and a Python > veteran but a BioPython newbie. > > I am writing this email because I would like to dedicate the final project > of my master's degree in bioinformatics to the development of a library to > implement gene annotation, pathway enrichment and access to gene ontologies > from Python, similar to how it can be done in R using functions like > enrichPathway from ReactomePA or enrichGo from ClusterProfiler. > > Have any tools been previously developed to do this using BioPython? Are > there any packages similar to Bioconductor's OrgDb, ReactomePA , GOSeq or > ClusterProfiler? > > I?m also working on a BioPython GUI based on PySide6. I've seen some old > projects related to BioPython GUI development but seem to be discontinued. > > I would be very happy to use my time to contribute to the bioPython > project, and I?m open to any suggestions or ideas. > > Thanks in advance, > > Ferran F?bregas > _______________________________________________ > Biopython mailing list - Biopython at biopython.org > https://mailman.open-bio.org/mailman/listinfo/biopython > -- Alexey Morozov, LIN SB RAS, bioinformatics group. Irkutsk, Russia. -------------- next part -------------- An HTML attachment was scrubbed... URL: From ferri.fc at gmail.com Mon Jan 3 10:06:36 2022 From: ferri.fc at gmail.com (=?UTF-8?Q?Ferran_F=C3=A0bregas?=) Date: Mon, 3 Jan 2022 16:06:36 +0100 Subject: [Biopython] Bioinformatics master's degree final project In-Reply-To: References: Message-ID: Thanks for your replies, it seems that the community prefers to use different bioinformatics related modules for different functionalities instead of one big, more complex module :) A couple of questions about that: Do you think that it makes sense adding some enrichment functions to biopython? Do you think that it can be useful to create a modular Python GUI that integrates biopython functionalities plus Bioservices / GoEnrich / etc... ? Or maybe it is not useful at all because you can already use some servers like the Galaxy project website (https://galaxyproject.org/)? What do you think about that? Thanks in advance, F On Mon, Jan 3, 2022 at 12:45 PM Alexey Morozov wrote: > Dear Ferran, > > There is a Python library for GO enrichment called goenrich ( > https://github.com/jdrudolph/goenrich). I haven't used it for the last > couple of years, but it did its job in 2018 or so (despite lacking some > tests available in eg topGO). OTOH, goenrich repo shows that the last > commit was in summer 2020, so maybe they've added something. Back when I > used it, BioPython integration was basically absent, they just used their > own objects for everything. > > There is also a library called goatools ( > https://github.com/tanghaibao/goatools), but I haven't actually used it, > so no comments. > > > ??, 3 ???. 2022 ?. ? 18:40, Ferran F?bregas : > >> Hi! My name is Ferran F?bregas and I'm working on my bioinformatics >> master?s degree final project. I?m a computer scientist and a Python >> veteran but a BioPython newbie. >> >> I am writing this email because I would like to dedicate the final >> project of my master's degree in bioinformatics to the development of a >> library to implement gene annotation, pathway enrichment and access to gene >> ontologies from Python, similar to how it can be done in R using functions >> like enrichPathway from ReactomePA or enrichGo from ClusterProfiler. >> >> Have any tools been previously developed to do this using BioPython? Are >> there any packages similar to Bioconductor's OrgDb, ReactomePA , GOSeq or >> ClusterProfiler? >> >> I?m also working on a BioPython GUI based on PySide6. I've seen some old >> projects related to BioPython GUI development but seem to be discontinued. >> >> I would be very happy to use my time to contribute to the bioPython >> project, and I?m open to any suggestions or ideas. >> >> Thanks in advance, >> >> Ferran F?bregas >> _______________________________________________ >> Biopython mailing list - Biopython at biopython.org >> https://mailman.open-bio.org/mailman/listinfo/biopython >> > > > -- > Alexey Morozov, > LIN SB RAS, bioinformatics group. > Irkutsk, Russia. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From p.j.a.cock at googlemail.com Mon Jan 3 13:07:21 2022 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 3 Jan 2022 18:07:21 +0000 Subject: [Biopython] Bioinformatics master's degree final project In-Reply-To: References: Message-ID: Hello Ferran, Personally I never saw the need for a Biopython GUI, and have used Galaxy instead for a web-based interface for many of my own scripts. Something for pathway enrichment could make sense for Biopython though, do you have a clearly defined idea in mind? Kind regards, Peter On Mon, Jan 3, 2022 at 3:06 PM Ferran F?bregas wrote: > > Thanks for your replies, it seems that the community prefers to use different bioinformatics related modules for different functionalities instead of one big, more complex module :) > > A couple of questions about that: > > Do you think that it makes sense adding some enrichment functions to biopython? > > Do you think that it can be useful to create a modular Python GUI that integrates biopython functionalities plus Bioservices / GoEnrich / etc... ? Or maybe it is not useful at all because you can already use some servers like the Galaxy project website (https://galaxyproject.org/)? > > What do you think about that? > > Thanks in advance, > > F From ferri.fc at gmail.com Mon Jan 3 15:23:40 2022 From: ferri.fc at gmail.com (=?UTF-8?Q?Ferran_F=C3=A0bregas?=) Date: Mon, 3 Jan 2022 21:23:40 +0100 Subject: [Biopython] Bioinformatics master's degree final project In-Reply-To: References: Message-ID: Hi Peter, Well, now I'm in the first stages of the research, because I need to make an initial proposal in one month approx, so I don't have yet a clear idea of what to do. I'm personally interested in pathway enrichment and I'm going to take a look at BioServices / GOenrich python packages and see their features, but If you think that adding pathway enrichment functionalities to Biopython can be interesting, I can go deep into it. Talking about the GUI, I understand that with Galaxy, maybe there's no need for a biopython GUI, but I think that can be interesting for educational purposes or more basic / on the fly needs. Galaxy can be overwhelming for quick jobs. One feature I was thinking about (maybe it's a little bit crazy) is that the GUI generates a Biopython script of your sequence of actions, so you can start using the GUI, download the script and then continue coding by yourself. This feature may not be very useful to professionals, but can be very helpful for students or newcomers. F On Mon, Jan 3, 2022 at 7:07 PM Peter Cock wrote: > Hello Ferran, > > Personally I never saw the need for a Biopython GUI, and have used > Galaxy instead for a web-based interface for many of my own scripts. > > Something for pathway enrichment could make sense for Biopython > though, do you have a clearly defined idea in mind? > > Kind regards, > > Peter > > On Mon, Jan 3, 2022 at 3:06 PM Ferran F?bregas wrote: > > > > Thanks for your replies, it seems that the community prefers to use > different bioinformatics related modules for different functionalities > instead of one big, more complex module :) > > > > A couple of questions about that: > > > > Do you think that it makes sense adding some enrichment functions to > biopython? > > > > Do you think that it can be useful to create a modular Python GUI that > integrates biopython functionalities plus Bioservices / GoEnrich / etc... > ? Or maybe it is not useful at all because you can already use some servers > like the Galaxy project website (https://galaxyproject.org/)? > > > > What do you think about that? > > > > Thanks in advance, > > > > F > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Pablo.RiesgoFerreiro at TrOn-Mainz.DE Mon Jan 3 15:36:06 2022 From: Pablo.RiesgoFerreiro at TrOn-Mainz.DE (Riesgo Ferreiro, Pablo) Date: Mon, 3 Jan 2022 20:36:06 +0000 Subject: [Biopython] Biopython Digest, Vol 227, Issue 1 In-Reply-To: References: Message-ID: <8a7276d534c04a71aa516ccf6095000b@TrOn-Mainz.DE> Dear Ferran, >From my experience of querying biomart from python, I found the implementations I used not very intuitive. It seems to me that some details of the biomart REST API (eg: XML) have leaked into the Python API. Maybe having a better Python API around biomart would add some value? Not saying it will be easy... Disclaimer: I am also a newbie in biopython so I would not know how or where this could be integrated. Best wishes, Pablo Riesgo Ferreiro ________________________________ From: Biopython on behalf of biopython-request at biopython.org Sent: 03 January 2022 16:06:49 To: biopython at biopython.org Subject: Biopython Digest, Vol 227, Issue 1 Send Biopython mailing list submissions to biopython at biopython.org To subscribe or unsubscribe via the World Wide Web, visit https://mailman.open-bio.org/mailman/listinfo/biopython or, via email, send a message with subject or body 'help' to biopython-request at biopython.org You can reach the person managing the list at biopython-owner at biopython.org When replying, please edit your Subject line so it is more specific than "Re: Contents of Biopython digest..." Today's Topics: 1. Bioinformatics master's degree final project (Ferran F?bregas) 2. Re: Bioinformatics master's degree final project (T?letch?a St?phane) 3. Re: Bioinformatics master's degree final project (Alexey Morozov) 4. Re: Bioinformatics master's degree final project (Ferran F?bregas) ---------------------------------------------------------------------- Message: 1 Date: Mon, 3 Jan 2022 11:39:40 +0100 From: Ferran F?bregas To: biopython at biopython.org Subject: [Biopython] Bioinformatics master's degree final project Message-ID: Content-Type: text/plain; charset="utf-8" Hi! My name is Ferran F?bregas and I'm working on my bioinformatics master?s degree final project. I?m a computer scientist and a Python veteran but a BioPython newbie. I am writing this email because I would like to dedicate the final project of my master's degree in bioinformatics to the development of a library to implement gene annotation, pathway enrichment and access to gene ontologies from Python, similar to how it can be done in R using functions like enrichPathway from ReactomePA or enrichGo from ClusterProfiler. Have any tools been previously developed to do this using BioPython? Are there any packages similar to Bioconductor's OrgDb, ReactomePA , GOSeq or ClusterProfiler? I?m also working on a BioPython GUI based on PySide6. I've seen some old projects related to BioPython GUI development but seem to be discontinued. I would be very happy to use my time to contribute to the bioPython project, and I?m open to any suggestions or ideas. Thanks in advance, Ferran F?bregas -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 2 Date: Mon, 3 Jan 2022 11:49:00 +0100 From: T?letch?a St?phane To: biopython at biopython.org Subject: Re: [Biopython] Bioinformatics master's degree final project Message-ID: Content-Type: text/plain; charset="us-ascii" An HTML attachment was scrubbed... URL: ------------------------------ Message: 3 Date: Mon, 3 Jan 2022 19:45:45 +0800 From: Alexey Morozov To: Ferran F?bregas Cc: biopython at biopython.org Subject: Re: [Biopython] Bioinformatics master's degree final project Message-ID: Content-Type: text/plain; charset="utf-8" Dear Ferran, There is a Python library for GO enrichment called goenrich ( https://github.com/jdrudolph/goenrich). I haven't used it for the last couple of years, but it did its job in 2018 or so (despite lacking some tests available in eg topGO). OTOH, goenrich repo shows that the last commit was in summer 2020, so maybe they've added something. Back when I used it, BioPython integration was basically absent, they just used their own objects for everything. There is also a library called goatools ( https://github.com/tanghaibao/goatools), but I haven't actually used it, so no comments. ??, 3 ???. 2022 ?. ? 18:40, Ferran F?bregas : > Hi! My name is Ferran F?bregas and I'm working on my bioinformatics > master?s degree final project. I?m a computer scientist and a Python > veteran but a BioPython newbie. > > I am writing this email because I would like to dedicate the final project > of my master's degree in bioinformatics to the development of a library to > implement gene annotation, pathway enrichment and access to gene ontologies > from Python, similar to how it can be done in R using functions like > enrichPathway from ReactomePA or enrichGo from ClusterProfiler. > > Have any tools been previously developed to do this using BioPython? Are > there any packages similar to Bioconductor's OrgDb, ReactomePA , GOSeq or > ClusterProfiler? > > I?m also working on a BioPython GUI based on PySide6. I've seen some old > projects related to BioPython GUI development but seem to be discontinued. > > I would be very happy to use my time to contribute to the bioPython > project, and I?m open to any suggestions or ideas. > > Thanks in advance, > > Ferran F?bregas > _______________________________________________ > Biopython mailing list - Biopython at biopython.org > https://mailman.open-bio.org/mailman/listinfo/biopython > -- Alexey Morozov, LIN SB RAS, bioinformatics group. Irkutsk, Russia. -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 4 Date: Mon, 3 Jan 2022 16:06:36 +0100 From: Ferran F?bregas To: biopython at biopython.org Subject: Re: [Biopython] Bioinformatics master's degree final project Message-ID: Content-Type: text/plain; charset="utf-8" Thanks for your replies, it seems that the community prefers to use different bioinformatics related modules for different functionalities instead of one big, more complex module :) A couple of questions about that: Do you think that it makes sense adding some enrichment functions to biopython? Do you think that it can be useful to create a modular Python GUI that integrates biopython functionalities plus Bioservices / GoEnrich / etc... ? Or maybe it is not useful at all because you can already use some servers like the Galaxy project website (https://galaxyproject.org/)? What do you think about that? Thanks in advance, F On Mon, Jan 3, 2022 at 12:45 PM Alexey Morozov wrote: > Dear Ferran, > > There is a Python library for GO enrichment called goenrich ( > https://github.com/jdrudolph/goenrich). I haven't used it for the last > couple of years, but it did its job in 2018 or so (despite lacking some > tests available in eg topGO). OTOH, goenrich repo shows that the last > commit was in summer 2020, so maybe they've added something. Back when I > used it, BioPython integration was basically absent, they just used their > own objects for everything. > > There is also a library called goatools ( > https://github.com/tanghaibao/goatools), but I haven't actually used it, > so no comments. > > > ??, 3 ???. 2022 ?. ? 18:40, Ferran F?bregas : > >> Hi! My name is Ferran F?bregas and I'm working on my bioinformatics >> master?s degree final project. I?m a computer scientist and a Python >> veteran but a BioPython newbie. >> >> I am writing this email because I would like to dedicate the final >> project of my master's degree in bioinformatics to the development of a >> library to implement gene annotation, pathway enrichment and access to gene >> ontologies from Python, similar to how it can be done in R using functions >> like enrichPathway from ReactomePA or enrichGo from ClusterProfiler. >> >> Have any tools been previously developed to do this using BioPython? Are >> there any packages similar to Bioconductor's OrgDb, ReactomePA , GOSeq or >> ClusterProfiler? >> >> I?m also working on a BioPython GUI based on PySide6. I've seen some old >> projects related to BioPython GUI development but seem to be discontinued. >> >> I would be very happy to use my time to contribute to the bioPython >> project, and I?m open to any suggestions or ideas. >> >> Thanks in advance, >> >> Ferran F?bregas >> _______________________________________________ >> Biopython mailing list - Biopython at biopython.org >> https://mailman.open-bio.org/mailman/listinfo/biopython >> > > > -- > Alexey Morozov, > LIN SB RAS, bioinformatics group. > Irkutsk, Russia. > -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Subject: Digest Footer _______________________________________________ Biopython mailing list - Biopython at biopython.org https://mailman.open-bio.org/mailman/listinfo/biopython ------------------------------ End of Biopython Digest, Vol 227, Issue 1 ***************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From ferri.fc at gmail.com Mon Jan 31 05:00:47 2022 From: ferri.fc at gmail.com (=?UTF-8?Q?Ferran_F=C3=A0bregas?=) Date: Mon, 31 Jan 2022 11:00:47 +0100 Subject: [Biopython] Bioinformatics node-red module based on BioPython Message-ID: Hi all, Based on the feedback you gave me a few weeks ago I've been thinking about leaving the GUI for BioPython and focusing on a BioPython-based workflow tool. I'm aware that the Galaxy project also has a workflow tool, but I've been thinking of using something more modular, flexible and cross-functional from an IT point of view, so I think node-red could be a great option. https://nodered.org/ Using node-red you could integrate a new bioinformatics module based on BioPython with thousands of workflow nodes of all kinds, allowing almost everything you can ever need, from access to any database engine, to using an API of anything you can imagine. For example you can implement, without the need for programming and using only the workflow interface, applications such as a public Telegram bioinformatic bot (maybe not very useful, but surely fun). But node-red is based on node.js, not Python :( Although I have been doing some research, and it is possible to run python scripts from node-red. Maybe another option would be to port BioPython to Javascript, facilitating the integration with node-red infrastructure. What do you think about using BioPython as a backend for a bioinformatics module for the node-red workflows? I also created a ultrabasic test module package for node-red using npm (using native JS) https://www.npmjs.com/package/node-red-contrib-biotools Kind regards, F -------------- next part -------------- An HTML attachment was scrubbed... URL: From p.j.a.cock at googlemail.com Mon Jan 31 07:21:52 2022 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 31 Jan 2022 12:21:52 +0000 Subject: [Biopython] Bioinformatics node-red module based on BioPython In-Reply-To: References: Message-ID: Hello Ferran, You might want to look at BioJS, http://biojs.net/ - although I think they are dormant now. To my mind you wouldn't be writing one module for such a workflow system, but dozens or more. For example, you could have a sequence file format converter (e.g. SFF to FASTQ), a multiple sequence alignment file format converted (e.g. PHYLIP to FASTA), a protein statistics tool (FASTA to TSV table), etc. Some of those would be quite simple, others would be lots of work for the person linking the Python code to the workflow interface. That's my impression based on having written quite a few Galaxy tools in Python - I would be surprised if this was dramatically different in any other workflow tool. For Galaxy I would start by defining a task as a command line tool written in Python using Biopython, then for Galaxy integration it is like wrapping any other command line tool. Peter On Mon, Jan 31, 2022 at 10:01 AM Ferran F?bregas wrote: > Hi all, > > Based on the feedback you gave me a few weeks ago I've been thinking about > leaving the GUI for BioPython and focusing on a BioPython-based workflow > tool. > > I'm aware that the Galaxy project also has a workflow tool, but I've been > thinking of using something more modular, flexible and cross-functional > from an IT point of view, so I think node-red could be a great option. > > https://nodered.org/ > > Using node-red you could integrate a new bioinformatics module based on > BioPython with thousands of workflow nodes of all kinds, allowing almost > everything you can ever need, from access to any database engine, to using > an API of anything you can imagine. > > For example you can implement, without the need for programming and using > only the workflow interface, applications such as a public Telegram > bioinformatic bot (maybe not very useful, but surely fun). > > But node-red is based on node.js, not Python :( Although I have been doing > some research, and it is possible to run python scripts from node-red. > > Maybe another option would be to port BioPython to Javascript, > facilitating the integration with node-red infrastructure. > > What do you think about using BioPython as a backend for a bioinformatics > module for the node-red workflows? > > I also created a ultrabasic test module package for node-red using npm > (using native JS) > > https://www.npmjs.com/package/node-red-contrib-biotools > > Kind regards, > > F > _______________________________________________ > Biopython mailing list - Biopython at biopython.org > https://mailman.open-bio.org/mailman/listinfo/biopython > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jocelyne at gmail.com Mon Jan 31 10:16:19 2022 From: jocelyne at gmail.com (Jocelyne) Date: Mon, 31 Jan 2022 07:16:19 -0800 Subject: [Biopython] Bioinformatics node-red module based on BioPython In-Reply-To: References: Message-ID: Hi Ferran, I personally only use biopython as a library and would rather build my workflow in a python based language, outside of biopython. I'd be cautious about workflow building. There seems to be 101 (figurative) existing languages (nextflow, snakemake, wdl come top of mind) with many different preferences. I think it's a decision best left to user. But I might not be understanding the intent of the feature well enough. Jocelyne -- sent from phone On Mon, Jan 31, 2022, 02:01 Ferran F?bregas wrote: > Hi all, > > Based on the feedback you gave me a few weeks ago I've been thinking about > leaving the GUI for BioPython and focusing on a BioPython-based workflow > tool. > > I'm aware that the Galaxy project also has a workflow tool, but I've been > thinking of using something more modular, flexible and cross-functional > from an IT point of view, so I think node-red could be a great option. > > https://nodered.org/ > > Using node-red you could integrate a new bioinformatics module based on > BioPython with thousands of workflow nodes of all kinds, allowing almost > everything you can ever need, from access to any database engine, to using > an API of anything you can imagine. > > For example you can implement, without the need for programming and using > only the workflow interface, applications such as a public Telegram > bioinformatic bot (maybe not very useful, but surely fun). > > But node-red is based on node.js, not Python :( Although I have been doing > some research, and it is possible to run python scripts from node-red. > > Maybe another option would be to port BioPython to Javascript, > facilitating the integration with node-red infrastructure. > > What do you think about using BioPython as a backend for a bioinformatics > module for the node-red workflows? > > I also created a ultrabasic test module package for node-red using npm > (using native JS) > > https://www.npmjs.com/package/node-red-contrib-biotools > > Kind regards, > > F > _______________________________________________ > Biopython mailing list - Biopython at biopython.org > https://mailman.open-bio.org/mailman/listinfo/biopython > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ferri.fc at gmail.com Mon Jan 31 11:16:24 2022 From: ferri.fc at gmail.com (=?UTF-8?Q?Ferran_F=C3=A0bregas?=) Date: Mon, 31 Jan 2022 17:16:24 +0100 Subject: [Biopython] Bioinformatics node-red module based on BioPython In-Reply-To: References: Message-ID: Thanks for the feedback, I will check the http://biojs.net/ project. With node-red, each module is divided in nodes, and each node gives some specific functionality, the idea is about creating one or more modules with several (dozens maybe) of individual nodes. My main problem is trying to avoid 'reinventing the wheel' and find something useful to do. This is hard because galaxy is a very big and flexible project, but, in the end, I think that node-red can give to the user useful and unique features like: - +3000 pre-packaged modules with almost any functionality you can imagine, especially in data interchange and data transformation. Not in Bioinformatics, of course, this will be my job :) - A flexible and customizable dashboard functionality, allowing to transform any workflow into an interactive online web application for the user. - The workflow architecture can be useful for some users. I've a video showing a concept demo of the biotools module for node-red. The audio is in spanish but the UI is in english and it's pretty easy to understand the concept viewing the video (5min) https://youtu.be/k7WsIQNgz8o Hope you find it interesting, F On Mon, Jan 31, 2022 at 4:16 PM Jocelyne wrote: > Hi Ferran, > I personally only use biopython as a library and would rather build my > workflow in a python based language, outside of biopython. > I'd be cautious about workflow building. There seems to be 101 > (figurative) existing languages (nextflow, snakemake, wdl come top of mind) > with many different preferences. I think it's a decision best left to user. > But I might not be understanding the intent of the feature well enough. > Jocelyne > > -- sent from phone > > On Mon, Jan 31, 2022, 02:01 Ferran F?bregas wrote: > >> Hi all, >> >> Based on the feedback you gave me a few weeks ago I've been thinking >> about leaving the GUI for BioPython and focusing on a BioPython-based >> workflow tool. >> >> I'm aware that the Galaxy project also has a workflow tool, but I've been >> thinking of using something more modular, flexible and cross-functional >> from an IT point of view, so I think node-red could be a great option. >> >> https://nodered.org/ >> >> Using node-red you could integrate a new bioinformatics module based on >> BioPython with thousands of workflow nodes of all kinds, allowing almost >> everything you can ever need, from access to any database engine, to using >> an API of anything you can imagine. >> >> For example you can implement, without the need for programming and using >> only the workflow interface, applications such as a public Telegram >> bioinformatic bot (maybe not very useful, but surely fun). >> >> But node-red is based on node.js, not Python :( Although I have been >> doing some research, and it is possible to run python scripts from node-red. >> >> Maybe another option would be to port BioPython to Javascript, >> facilitating the integration with node-red infrastructure. >> >> What do you think about using BioPython as a backend for a bioinformatics >> module for the node-red workflows? >> >> I also created a ultrabasic test module package for node-red using npm >> (using native JS) >> >> https://www.npmjs.com/package/node-red-contrib-biotools >> >> Kind regards, >> >> F >> _______________________________________________ >> Biopython mailing list - Biopython at biopython.org >> https://mailman.open-bio.org/mailman/listinfo/biopython >> > -------------- next part -------------- An HTML attachment was scrubbed... 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