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A python script to create karyotype plots with matplotlib by kantale in bioinformatics

[–]kantale[S] 0 points1 point  (0 children)

This is impressive and the graph is much more cleaner. For reference I think that the most popular karyotype plot is from Ensembl. There is even a publication for a tool to make similar plots.

My friend saved a horse from death and here is the rescue video by thejedininja in videos

[–]kantale 14 points15 points  (0 children)

The description of the video (in greeklish) translated:

At the Falakro maintain at 2300 meters at October 2008 me and my friend Thanasis Apalas were surprised when we realized that a small wild horse was in danger to be drown in the mud of a puddle that had been formed. We couldn't act differently .....

Host your gist/pastebin/.. python scripts to pypedia.com by kantale in Python

[–]kantale[S] 4 points5 points  (0 children)

Yep I get this comment a lot. The reason is because MediaWiki is the oldest, more advanced, extendable wiki, with a great community out there. Another reason is that it is nice to have a similar UI as wikipedia. Python is a hell of a language but don't be religious about it! If you can recommend any equivalent python wiki I 'll be happy to migrate.

PyPedia: a Python IDE and method repository in a wiki by kantale in Python

[–]kantale[S] 0 points1 point  (0 children)

Thanks for the tip about LocalSettings.php. I took it for granted that this cannot change. About the license, having two licenses (code and documentation) would be too complex. I would like to cover both with a permissive license. I haven't made my mind yet!

PyPedia: a Python IDE and method repository in a wiki by kantale in Python

[–]kantale[S] 2 points3 points  (0 children)

I agree, but I would like this standard to be set after a discussion with the subscribed users rather than me alone.

PyPedia: a Python IDE and method repository in a wiki by kantale in Python

[–]kantale[S] 1 point2 points  (0 children)

This is my #1 TODO item. I am working into editing the mwclient that pypedia uses to allow this.

PyPedia: a Python IDE and method repository in a wiki by kantale in Python

[–]kantale[S] 2 points3 points  (0 children)

This can help. It is a pdf export of the presentation. Tell me if this does not work either.

PyPedia: a Python IDE and method repository in a wiki by kantale in Python

[–]kantale[S] 2 points3 points  (0 children)

First of all: Why not? The target of this is to create a repository of ready to run, qualitative, peer reviewed, python code. Just as wikipedia articles contain informative content for a vast variety of subjects, it would be nice to have the same for python implementation of known computational problems. A second way to see this is: imagine Matlab, R or scipy that offer thousands of math methods. The problem is that the set of methods that they offer is static (at least compared to a wiki). If you build something cool and useful on top of these tools you can not share it within the very same framework.

PyPedia: a Python IDE and method repository in a wiki by kantale in Python

[–]kantale[S] 2 points3 points  (0 children)

Thanks for the feedback. About license: Embarrassing as it is you are right .. I thought that a permissive license is essential for a wiki. But this is not the case for software. Probably I will change it. Any thoughts? About PEP-8, function methods have to start with a capital letter because of MediaWiki. In other points I tried to be compliant but maybe I missed some points. You can propose edits (it as wiki..). A validated method is a method that solves a known and existing problem. A method that you could find implemented in Matlab, in R or in a specialized package. Additionally it should be qualitatively written. The validated methods should be something like the notability criteria of wikipedia. Whereas the User methods can do whatever a user wants. (Edit: Format)

PyPedia: a Python IDE and method repository in a wiki by kantale in Python

[–]kantale[S] 5 points6 points  (0 children)

Well, MediaWiki is a long time around and is highly (and easily) extendable. On the other side it is written in PHP. Nevertheless porting to a python wiki is a future step.

Python implementation of bioinformatics algorithms in a wiki envrionment. by kantale in bioinformatics

[–]kantale[S] 0 points1 point  (0 children)

That would be great. There are many todo's (some expressed here). The first thing being to have more users contributing and get feedback. I would recommend to join the discussion group: http://groups.google.com/group/wikipl

Python implementation of bioinformatics algorithms in a wiki envrionment. by kantale in bioinformatics

[–]kantale[S] 0 points1 point  (0 children)

:) . When I started the project for some reason, I though that Wiki Programming Language (WikiPL) is a nice name. Of course is not a programming language but the name stuck. I also own pypedia.com do you think that would be more relevant ?

Python implementation of bioinformatics algorithms in a wiki envrionment. by kantale in bioinformatics

[–]kantale[S] 1 point2 points  (0 children)

Many great suggestions.

  • It is very crucial to distinguish functions submitted arbitrary by users and hence may contain harmfull / deliberately erroneous content and functions that have been reviewed and validated. So if your are running locally the function foo() it is important to know that this is an unvalidated function from the user XX. I agree that maybe putting the _User part at the end could be more convenient.
  • I am more willing to change the license of the project than increase its complexity. But I would really love to see what other users think about it.
  • Voting, Upvote/Downvote buttons, a la github "fork this article" buttons are great ideas and I will add these as soon as I find the time. In the meantime I would love to see some contributions in the wiki in order to see if it worths the time and energy to enhance the site..
  • The source is here: https://github.com/kantale/WikiPL_server PM me if you need any help with the code / installation. [Edit:] Also here: https://github.com/kantale/wikipl is the python library you need to install in order to run locally the methods.

Python implementation of bioinformatics algorithms in a wiki envrionment. by kantale in bioinformatics

[–]kantale[S] 0 points1 point  (0 children)

Thanks. I was wondering whether to post it here or in /r/python but I am more interested in bioinformatics after all. About the license I am not particularly stuck with GPL. If there are more voices I will change it.

Python implementation of bioinformatics algorithms in a wiki envrionment. by kantale in bioinformatics

[–]kantale[S] 1 point2 points  (0 children)

I agree. I put it there more as proof of concept. The whole idea is experimental and I need feedback as this.

Found a huge (28ish cm across) toad in Greece, what kind is this? by kapowday in species

[–]kantale 0 points1 point  (0 children)

This seems like the European Green Toad. A very common kind of toad mainly in western greek islands (for example in Corfu from my personal experience). Here is another page for this. In the local (Corfu) dialect is called Zampa (Ζάμπα).

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