[web2py] Re: GSOC 2011 - BioChemical Reaction Network Visualization - web2py
can you summarize for us, what is done, what needs to be done. so far we have experiences visualizing biochemical networks with tools like Cytoscape, Graphviz, ... we even wrote our own web2py plugin to create force directed graphs http://groups.google.com/group/web2py/browse_thread/thread/d9c5b9ef9ddf2e49/63cec30770d1ef9f?lnk=gst and we have drawn tons of network images by hand, but this is not enough, what we really need is 1) a fast layout algorithm that creates good layout for biochemical graphs (better than force directed, ...) 2) a js library that renders these layouts in a standard compiant way in SVG, - so far the only standard for drawing biochemical networks out there is SBGN (http://sbgn.org/Main_Page see here for some examples) and we intend to use that - SVG images because the can be displayed in a browser (http:// slides.html5rocks.com/) - SVG images can be edited with (e.g. Inkskape) and that is crucial since no layout algorithm will generate images good enough for publications, wikipeda, ... 3) a communication layer that calls our new layout algorithm (and possibly others that are available) and uses the js lib to show the result in a browser, this is where web2py could act as the communication layer 4) an extension to the js library 2) so that the images can edited on the web (this will also have to communicate to 3) somehow) - this lowers the border for people to create standard compliant images 5) an extension to the communication layer 3) so that it access all kinds of databases that contain biochemical reaction networks and visualizes them (we have plenty of experinces with that, but it is hard work every time you want to do something like that) you probably see that all the ideas depend on each other and that some of the steps can be unified/done by one developer so far a lot of people are interested in 1) and also some in 2) but for 3) we there was nobody really showing much interest The development will start from scratch but we a optimistic that we will have some good results within the two month with a team of 3 students and about 6 mentors Finally I should mention that we have a experience in using web2py (http://pymantis.org/ http://semanticsbml.org/semanticSBML/ http://sysbio-goods.org/ ...) and other tools and programming languages (some of the tools developed in our group: http://www2.hu-berlin.de/biologie/theorybp/index.php?goto=tools)
[web2py] Re: GSOC 2011 - BioChemical Reaction Network Visualization - web2py
we are still looking for people that help us with Idea3 if you do not want to join you could help us find someone with web2py skills by retweeting this message: http://twitter.com/#!/rockdapus/status/53396283687313408 otherwise it might be done in django or some non python framework ... o_O On Mar 22, 3:59 pm, selecta gr...@delarue-berlin.de wrote: Hi web2py coders, I am very happy to tell you that my group - Theoretical Biophysics at the HU-Berlin - got selected for a mentoring program for the GSOC2011 (http://code.google.com/soc/). We want to create an new layout algorithm for biochemical reaction networks, a visualization of the reaction network using SVG and SBGN and a web based (js) SVG editor for the reaction networks. One of the software tools that we would need is a communication layer that brings the graph visualization to the browser. Since we develop a lot of software in our group with the help of web2py it would be great if one of you would be interested in helping us to achieve our vision. The work will have to be done within two month during the summer and you would get payed a nice amount of money by google. You will find more information about ourGSOCproject herehttp://rumo.biologie.hu-berlin.de/gsoc/(read especially Idea 3) If you are interested and you want to discuss ideas with us joinhttp://groups.google.com/group/tbp-soc2011-stud Please be aware that if you want to join you should bring some coding skills. In addition to that please be aware that Idea 3 does not have the highest priority since it depends on other components (layout algorithm and SVG rendering) which some of you might also be interested in.
[web2py] Re: GSOC 2011 - BioChemical Reaction Network Visualization - web2py
done. can you summarize for us, what is done, what needs to be done. On Mar 31, 5:23 am, selecta gr...@delarue-berlin.de wrote: we are still looking for people that help us with Idea3 if you do not want to join you could help us find someone with web2py skills by retweeting this message:http://twitter.com/#!/rockdapus/status/53396283687313408 otherwise it might be done in django or some non python framework ... o_O On Mar 22, 3:59 pm, selecta gr...@delarue-berlin.de wrote: Hi web2py coders, I am very happy to tell you that my group - Theoretical Biophysics at the HU-Berlin - got selected for a mentoring program for the GSOC2011 (http://code.google.com/soc/). We want to create an new layout algorithm for biochemical reaction networks, a visualization of the reaction network using SVG and SBGN and a web based (js) SVG editor for the reaction networks. One of the software tools that we would need is a communication layer that brings the graph visualization to the browser. Since we develop a lot of software in our group with the help of web2py it would be great if one of you would be interested in helping us to achieve our vision. The work will have to be done within two month during the summer and you would get payed a nice amount of money by google. You will find more information about ourGSOCproject herehttp://rumo.biologie.hu-berlin.de/gsoc/(readespecially Idea 3) If you are interested and you want to discuss ideas with us joinhttp://groups.google.com/group/tbp-soc2011-stud Please be aware that if you want to join you should bring some coding skills. In addition to that please be aware that Idea 3 does not have the highest priority since it depends on other components (layout algorithm and SVG rendering) which some of you might also be interested in.
[web2py] Re: GSOC 2011 - BioChemical Reaction Network Visualization - web2py
Congratulations! On Mar 22, 8:59 am, selecta gr...@delarue-berlin.de wrote: Hi web2py coders, I am very happy to tell you that my group - Theoretical Biophysics at the HU-Berlin - got selected for a mentoring program for the GSOC2011 (http://code.google.com/soc/). We want to create an new layout algorithm for biochemical reaction networks, a visualization of the reaction network using SVG and SBGN and a web based (js) SVG editor for the reaction networks. One of the software tools that we would need is a communication layer that brings the graph visualization to the browser. Since we develop a lot of software in our group with the help of web2py it would be great if one of you would be interested in helping us to achieve our vision. The work will have to be done within two month during the summer and you would get payed a nice amount of money by google. You will find more information about our GSOC project herehttp://rumo.biologie.hu-berlin.de/gsoc/(read especially Idea 3) If you are interested and you want to discuss ideas with us joinhttp://groups.google.com/group/tbp-soc2011-stud Please be aware that if you want to join you should bring some coding skills. In addition to that please be aware that Idea 3 does not have the highest priority since it depends on other components (layout algorithm and SVG rendering) which some of you might also be interested in.
[web2py] Re: GSoC
Inspired by http://groups.google.com/group/web2py/browse_thread/thread/cfb0ed89924c3b5e# I wonder if it is possible to provide performance analytics of some sorts in web2py? If it is, I think it could be a worthwhile GSOC project. On Feb 17, 7:03 am, Massimo Di Pierro massimo.dipie...@gmail.com wrote: We need proposals. What do we want to be done? On Feb 16, 2:57 pm, Tim Michelsen timmichel...@gmx-topmail.de wrote: Hello, is web2py considering to mentor for this year? http://code.google.com/intl/de-DE/soc/ Regards, Timmie
[web2py] Re: GSOC who is in charge and how should we proceed?
We need get our applications in very soon so let's get cracking! Who is in charge of this and how can I help? Shall we collect Ideas on the google code wiki and then vote? Do we have a wiki for this somewhere? I think we could just gather then here on the list then make a page ready for the proposal that documents do idea. (If I remember it is a plus to have when applying.) So where is that stuff going?
[web2py] Re: GSOC who is in charge and how should we proceed?
I am very excited for GSOC as I was an achiever back in 2009. It changed my career forever. http://www.google-melange.com/document/show/gsoc_program/google/gsoc2011/timeline We need get our applications in very soon so let's get cracking! Who is in charge of this and how can I help? Shall we collect Ideas on the google code wiki and then vote?
[web2py] Re: GSOC who is in charge and how should we proceed?
I cannot work on this for another week. After that I am all for it and I will send my comments about the proposed goals. Some are interesting. I do not think voting is a good idea since feasibility is also important. I would like to add one option. Build a social and modular web2py Learning Management System that runs on GAE. Some of the other projects that have been proposed could be components of the LMS and also work independently. Massimo On Feb 20, 4:25 am, Tim Michelsen timmichel...@gmx-topmail.de wrote: I am very excited for GSOC as I was an achiever back in 2009. It changed my career forever. http://www.google-melange.com/document/show/gsoc_program/google/gsoc2... We need get our applications in very soon so let's get cracking! Who is in charge of this and how can I help? Shall we collect Ideas on the google code wiki and then vote?
Re: [web2py] Re: GSOC who is in charge and how should we proceed?
On 02/20/2011 06:04 PM, Massimo Di Pierro wrote: I cannot work on this for another week. After that I am all for it and I will send my comments about the proposed goals. Some are interesting. I do not think voting is a good idea since feasibility is also important. I totally agree. A team of core developers and those familiar with web2py framework should make the choices on this one. BR, Jason I would like to add one option. Build a social and modular web2py Learning Management System that runs on GAE. Some of the other projects that have been proposed could be components of the LMS and also work independently. Massimo On Feb 20, 4:25 am, Tim Michelsentimmichel...@gmx-topmail.de wrote: I am very excited for GSOC as I was an achiever back in 2009. It changed my career forever. http://www.google-melange.com/document/show/gsoc_program/google/gsoc2... We need get our applications in very soon so let's get cracking! Who is in charge of this and how can I help? Shall we collect Ideas on the google code wiki and then vote?
Re: [web2py] Re: GSOC who is in charge and how should we proceed?
On 02/20/2011 12:25 PM, Tim Michelsen wrote: I am very excited for GSOC as I was an achiever back in 2009. It changed my career forever. http://www.google-melange.com/document/show/gsoc_program/google/gsoc2011/timeline We need get our applications in very soon so let's get cracking! Who is in charge of this and how can I help? Shall we collect Ideas on the google code wiki and then vote? Do we have a wiki for this somewhere? I think we could just gather then here on the list then make a page ready for the proposal that documents do idea. (If I remember it is a plus to have when applying.) BR, Jason
[web2py] Re: GSoC
Eh, why wait for someone else to make a widget - wrote a slice for my version http://web2pyslices.com/main/slices/take_slice/121
[web2py] Re: GSoC
App profiling? https://groups.google.com/forum/?pli=1#!topic/web2py/z7DtiZJMO14
[web2py] Re: GSoC
We need proposals. What do we want to be done? Geographic features for the DAL like at GeoDjango http://docs.djangoproject.com/en/dev/ref/contrib/gis/ This would mean that someone comes and adds support for the following spatial extensions: * PostGIS (PostgreSQL) * Spatialite (SQLite) * GeoCouch (CouchDB) = IMHO one of the few bid database features still missing.
[web2py] Re: GSoC
How about setting up some real solid documentation with Sphinx? We tried that earlier on. Was more or less discarded. also building docs is not easy as there are windows and linux specifc modules. and Sphinx needs to be able to import them all.
[web2py] Re: GSoC
It'd be cool if the book was in version control and could be forked. Also, the docstring pages are almost unreadable.
Re: [web2py] Re: GSoC
A CMS based on the zotonic[1] (for example) interface. Or just a killer CMS instantpress could be a good base. [1] http://zotonic.com/gallery/735/screen-shot-gallery On Thu, Feb 17, 2011 at 5:14 AM, Thadeus Burgess thade...@thadeusb.comwrote: statistics engine = statlib -- Thadeus On Wed, Feb 16, 2011 at 9:22 PM, Jason Brower encomp...@gmail.com wrote: Local editor integration and permenent admin settings for that and other features. - Original message - We need proposals. What do we want to be done? On Feb 16, 2:57 pm, Tim Michelsen timmichel...@gmx-topmail.de wrote: Hello, is web2py considering to mentor for this year? http://code.google.com/intl/de-DE/soc/ Regards, Timmie
Re: [web2py] Re: GSoC
New CRUD or SQLFORM API that decoupled one form and one table model of functioning more easily in many differents scenarios... For many to many relation for example it is rare that you want to add only one relation at a time. When 2 tables are related many to many there should be a CRUD automatically generated form that respond to 90% of the needs... Or that you can configure the CRUD API to make it works differently under different use case... Subform with normalized schema so you can add any number of input on the fly that will be store in the subtable into a one to many relation with the base form table. Improve plain text search Richard On Thu, Feb 17, 2011 at 9:45 AM, Albert Abril albert.ab...@gmail.comwrote: A CMS based on the zotonic[1] (for example) interface. Or just a killer CMS instantpress could be a good base. [1] http://zotonic.com/gallery/735/screen-shot-gallery On Thu, Feb 17, 2011 at 5:14 AM, Thadeus Burgess thade...@thadeusb.comwrote: statistics engine = statlib -- Thadeus On Wed, Feb 16, 2011 at 9:22 PM, Jason Brower encomp...@gmail.comwrote: Local editor integration and permenent admin settings for that and other features. - Original message - We need proposals. What do we want to be done? On Feb 16, 2:57 pm, Tim Michelsen timmichel...@gmx-topmail.de wrote: Hello, is web2py considering to mentor for this year? http://code.google.com/intl/de-DE/soc/ Regards, Timmie
[web2py] Re: GSoC
Maybe get started on some of these ideas: https://groups.google.com/d/msg/web2py-developers/55_7Kr3jDjI/0008xQ036uYJ (either as a separate framework, or preferably, somehow integrated into web2py, maybe as an alternative development model). Other ideas: - Full-text search (maybe an abstraction layer with pluggable search backends, like http://haystacksearch.org/, http://code.google.com/p/django-fts/) - Integrated Comet and WebSockets support ( http://seventhings.liftweb.net/comet, http://zotonic.com/page/625/websockets-comet) - Integrated unit, functional, and performance/load testing ( http://pypi.python.org/pypi/funkload, http://code.google.com/p/multi-mechanize/) - Expanded NoSQL support. Anthony On Wednesday, February 16, 2011 6:03:40 PM UTC-5, Massimo Di Pierro wrote: We need proposals. What do we want to be done? On Feb 16, 2:57 pm, Tim Michelsen timmic...@gmx-topmail.de wrote: Hello, is web2py considering to mentor for this year? http://code.google.com/intl/de-DE/soc/ Regards, Timmie
Re: [web2py] Re: GSoC
A component library rooted on LOAD. Pages would be made by components sibiling or nested. MVC pattern applied then not to the page but component oriented. 2011/2/17 Anthony abasta...@gmail.com: Maybe get started on some of these ideas: https://groups.google.com/d/msg/web2py-developers/55_7Kr3jDjI/0008xQ036uYJ (either as a separate framework, or preferably, somehow integrated into web2py, maybe as an alternative development model). Other ideas: Full-text search (maybe an abstraction layer with pluggable search backends, like http://haystacksearch.org/, http://code.google.com/p/django-fts/) Integrated Comet and WebSockets support (http://seventhings.liftweb.net/comet, http://zotonic.com/page/625/websockets-comet) Integrated unit, functional, and performance/load testing (http://pypi.python.org/pypi/funkload, http://code.google.com/p/multi-mechanize/) Expanded NoSQL support. Anthony On Wednesday, February 16, 2011 6:03:40 PM UTC-5, Massimo Di Pierro wrote: We need proposals. What do we want to be done? On Feb 16, 2:57 pm, Tim Michelsen timmic...@gmx-topmail.de wrote: Hello, is web2py considering to mentor for this year? http://code.google.com/intl/de-DE/soc/ Regards, Timmie
Re: [web2py] Re: GSoC
I'd love to see 1) WordPress copy and 2) Vbulletin/FluxBB/etc copy. No fancy UIs. Keep it simple.
[web2py] Re: GSoC
Include a built-in widget like the options_with_add_link slice (http://web2pyslices.com/main/slices/take_slice/11) to allow one to quickly add a new record into to a referenced table without having to go to a separate screen. Perhaps it's not glamorous but its presence might make adoption easier for new folks and could help bring web2py's CRUD/SQLFORM closer to the admin provided by django.
[web2py] Re: GSoC
Yes, a blog for GAE could be a killer app - a free blogging platform, particularly attractive to people in China who are blocked from using Wordpress.com. Our killer blog app would be based on InstantPress, of course, but its admin interface would have to work like Wordpress, just as OpenOffice has to work like Microsoft Office. Whatever people are used to becomes the standard, and departing from that hurts usability. On Feb 17, 2:10 pm, pbreit pbreitenb...@gmail.com wrote: I'd love to see 1) WordPress copy and 2) Vbulletin/FluxBB/etc copy. No fancy UIs. Keep it simple.
[web2py] Re: GSoC
InstantPress is nice but the UI is a little too fancy for me. No reason to re-invent the wheel here.
Re: [web2py] Re: GSoC
How about setting up some real solid documentation with Sphinx? It is low hanging fruit, but I think getting some good documentation set up would help the web2py community directly. I don't know the current testing coverage percentages now, but getting those to 90%-100% might be another good one. Cheers, James Hancock On Fri, Feb 18, 2011 at 9:39 AM, pbreit pbreitenb...@gmail.com wrote: InstantPress is nice but the UI is a little too fancy for me. No reason to re-invent the wheel here.
[web2py] Re: GSoC
We need proposals. What do we want to be done? On Feb 16, 2:57 pm, Tim Michelsen timmichel...@gmx-topmail.de wrote: Hello, is web2py considering to mentor for this year? http://code.google.com/intl/de-DE/soc/ Regards, Timmie
Re: [web2py] Re: GSoC
Some ideas: Mangodb support Improved wizard tool Improved plugin_wiki statistics engine - Original message - We need proposals. What do we want to be done? On Feb 16, 2:57 pm, Tim Michelsen timmichel...@gmx-topmail.de wrote: Hello, is web2py considering to mentor for this year? http://code.google.com/intl/de-DE/soc/ Regards, Timmie
Re: [web2py] Re: GSoC
Local editor integration and permenent admin settings for that and other features. - Original message - We need proposals. What do we want to be done? On Feb 16, 2:57 pm, Tim Michelsen timmichel...@gmx-topmail.de wrote: Hello, is web2py considering to mentor for this year? http://code.google.com/intl/de-DE/soc/ Regards, Timmie
Re: [web2py] Re: GSoC
statistics engine = statlib -- Thadeus On Wed, Feb 16, 2011 at 9:22 PM, Jason Brower encomp...@gmail.com wrote: Local editor integration and permenent admin settings for that and other features. - Original message - We need proposals. What do we want to be done? On Feb 16, 2:57 pm, Tim Michelsen timmichel...@gmx-topmail.de wrote: Hello, is web2py considering to mentor for this year? http://code.google.com/intl/de-DE/soc/ Regards, Timmie
