[sage-devel] Re: Sage accepted for GSoC 2014

2014-02-26 Thread Dima Pasechnik
On 2014-02-26, mmarco  wrote:
> In my case, i needed to also change the knostcape script to point to the 
> actual directory, instead of a directory of /tmp

sure. 
>

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[sage-devel] Re: Sage accepted for GSoC 2014

2014-02-26 Thread mmarco
In my case, i needed to also change the knostcape script to point to the 
actual directory, instead of a directory of /tmp

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[sage-devel] Re: Sage accepted for GSoC 2014

2014-02-26 Thread Dima Pasechnik
On 2014-02-26, mmarco  wrote:
> Thanks for the link. I have tried to compile it, but got this error message:
>
> /usr/bin/ld: cannot open output file ./bin/knotfind: No such file or 
> directory
> collect2: error: ld returned 1 exit status
> make: *** [knotfind] Error 1
>
I see. Make an empty directory bin/ in ./ before
doing "make all".

Then it will work.
On platforms I checked bin/ is created on the fly...
I'll fix this in the repo.

>
> El martes, 25 de febrero de 2014 23:17:56 UTC+1, Dima Pasechnik escribió:
>>
>> On 2014-02-25, mmarco > wrote: 
>> > I would be happy to mentor a student in a knot theory related project in 
>> > sage. I had mainly two ideas: 
>> > 
>> > First idea is to write a class for knots/links. This class should be 
>> able 
>> > to translate between the different possible representations of links 
>> (Gauss 
>> > codes, 3d curves, braid closure...) and compute some of their invariants 
>> > (the usual polynomials, Seifert forms, fundamental groups...). It should 
>> > also produce pictures of knot diagrams and 3d representations of the 
>> > knot/link. Some (or most) of this features can be either written from 
>> > scratch, or just wrap external code (like the mentioned SnapPy). 
>>
>> perhaps one can try to incorporate parts of knotscape into Sage. 
>> Well, it's kind of old, but still works: 
>> https://github.com/dimpase/knotscap 
>> (incidentally, a colleague wanted to use knotscape on a modern Linux 
>> system, so I did these small fixes for him) 
>>
>>
>> > 
>> > Another idea, closely related to the previous one, is to write a 
>> javascript 
>> > editor for knots and links, following what knotplot [1] does. This can 
>> be 
>> > part of the same project or a separated one, if someone else writes the 
>> > backend (although i think that it should be possible to write the editor 
>> > and a simple backend in a single gsoc project, but that can be 
>> discussed). 
>> > An important part of this editor would be the algorithm for dynamically 
>> > relaxing the link. In particular, such an algorithm is explained in 
>> chapter 
>> > 7 of Scharein's thesis [1]. 
>> > 
>> > [1] http://www.knotplot.com/thesis/thesis.html 
>> > 
>>
>>
>

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Re: [sage-devel] Re: Sage accepted for GSoC 2014

2014-02-26 Thread mmarco
Of course, i forgot to mention the already mentioned knotscape, snappy and 
knotplot.

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[sage-devel] Re: Sage accepted for GSoC 2014

2014-02-26 Thread mmarco
Thanks for the link. I have tried to compile it, but got this error message:

/usr/bin/ld: cannot open output file ./bin/knotfind: No such file or 
directory
collect2: error: ld returned 1 exit status
make: *** [knotfind] Error 1


El martes, 25 de febrero de 2014 23:17:56 UTC+1, Dima Pasechnik escribió:
>
> On 2014-02-25, mmarco > wrote: 
> > I would be happy to mentor a student in a knot theory related project in 
> > sage. I had mainly two ideas: 
> > 
> > First idea is to write a class for knots/links. This class should be 
> able 
> > to translate between the different possible representations of links 
> (Gauss 
> > codes, 3d curves, braid closure...) and compute some of their invariants 
> > (the usual polynomials, Seifert forms, fundamental groups...). It should 
> > also produce pictures of knot diagrams and 3d representations of the 
> > knot/link. Some (or most) of this features can be either written from 
> > scratch, or just wrap external code (like the mentioned SnapPy). 
>
> perhaps one can try to incorporate parts of knotscape into Sage. 
> Well, it's kind of old, but still works: 
> https://github.com/dimpase/knotscap 
> (incidentally, a colleague wanted to use knotscape on a modern Linux 
> system, so I did these small fixes for him) 
>
>
> > 
> > Another idea, closely related to the previous one, is to write a 
> javascript 
> > editor for knots and links, following what knotplot [1] does. This can 
> be 
> > part of the same project or a separated one, if someone else writes the 
> > backend (although i think that it should be possible to write the editor 
> > and a simple backend in a single gsoc project, but that can be 
> discussed). 
> > An important part of this editor would be the algorithm for dynamically 
> > relaxing the link. In particular, such an algorithm is explained in 
> chapter 
> > 7 of Scharein's thesis [1]. 
> > 
> > [1] http://www.knotplot.com/thesis/thesis.html 
> > 
>
>

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Re: [sage-devel] Re: Sage accepted for GSoC 2014

2014-02-26 Thread mmarco
Nice work of documentation. Here is some further documentation that could 
be interesting:

About methods to compute alexander polynomials, the classical result is 
Theorem 3.11 from Birman's book (note that this is basically what you said, 
since the burau representation is deeply related to the Fox derivatives of 
the relations given by the action of the braid on the free group):
http://books.google.de/books?id=thv7L4AQ3J4C&printsec=frontcover&hl=es&source=gbs_ge_summary_r&cad=0#v=onepage&q&f=false
This is an easy introduction to three different methods to compute 
Alexander Polynomials:
https://www.google.de/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&ved=0CCkQFjAA&url=http%3A%2F%2Fwww.ucl.ac.uk%2F~ucbpeal%2Falexandermac.pdf&ei=9uQNU_fLA4mHtAa7roGoBQ&usg=AFQjCNEQEoaWGCkv1MhFLuz7qADnJ29zQg&sig2=cVCQv8y0eSRh_cryPaSKHQ&bvm=bv.61965928,d.Yms

There is plenty of documentation for other invariants too. 

Note also that there are plenty of external software that can do 
computations with knots and links. It would also be interesting to study 
the possibility of wrapping them instead of rewriting the methods. It is 
true that some of them are old and no longer mantained, but it might be 
worth taking a look nevertheless.
Some links for this: 
http://www.math.kobe-u.ac.jp/~kodama/knot.html
http://burtleburtle.net/bob/knot/homfly.html
http://www.math.uic.edu/t3m/
http://www.liv.ac.uk/~su14/knotprogs.html

Also it could be possible to use some method based on Skein relations, but 
i am not sure how good it would work.


El martes, 25 de febrero de 2014 22:38:20 UTC+1, Amit Jamadagni escribió:
>
> I have been going through the implementation Knot Atlas, as per my 
> understanding they have stored the knots in a table and have inputted it to 
> get various results, I would like to know whether we will be using tables 
> to input or any other way to input. I have seen through Vogel's algorithm 
>  which takes in the oriented gauss code and ends up giving out the braid 
> word [1] from which we can construct the knot(as it is closed braid) and 
> from the braid word we can calculate the Alexander polynomial from the 
> Burau's representation(which is currently implemented in braid in Sage) (I 
> have heard is not true for strings greater than 5). I have been reading 
> through [2] which mentions how to calculate Seifert matrix from a braid 
> representation which can be again used to represent knots. I have been 
> searching for algorithms which would relate the Seifert matrix and various 
> invariants. It would be really helpful if I could get more reference to the 
> algorithms that could be implemented. I have just started the 
> implementation details mentioned in [3]. 
>
> [1] http://magma.maths.usyd.edu.au/~danr/site/talks/20070531.pdf
> [2] http://www.maths.ed.ac.uk/~jcollins/SeifertMatrix/SeifertMatrix.pdf
> [3] http://www.layer8.co.uk/maths/braids/braid-user-documentation.html
>
> On Tue, Feb 25, 2014 at 7:16 PM, kcrisman 
> > wrote:
>
>>
>>>
>>> [2] http://legacy.earlham.edu/~peters/knotlink.htm#software 
>>>
>>>
>> *"June 2, 2004*. Unfortunately I no longer have time to update *Knots on 
>> the Web*. I know it conntains many dead links and omits many good, new 
>> sites. "
>>
>> And my understanding is that the Knot Atlas 
>> http://katlas.math.toronto.edu/wiki/Main_Page and the Mathematica 
>> package creating it is the state of the art.  Does SnapPy now really have 
>> all that combinatorial stuff?  I think that at the very least a good 
>> wrapper allowing for use of *any* robust backend for knots would be a great 
>> contribution to Sage.  mmarco seems to have a good sense of what would 
>> actually be needed to do this.  It's definitely a significant hole in Sage. 
>> - one might even wonder whether the authors of the Mma package would be 
>> willing to license their package in such a way that the algorithms for 
>> computing various invariants etc. could be used/{P,C}ythonized in Sage, if 
>> some people know them http://katlas.math.toronto.edu/wiki/Acknowledgement
>>  
>> -- 
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>
>

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[sage-devel] Re: Sage accepted for GSoC 2014

2014-02-25 Thread Dima Pasechnik
On 2014-02-25, mmarco  wrote:
> I would be happy to mentor a student in a knot theory related project in 
> sage. I had mainly two ideas:
>
> First idea is to write a class for knots/links. This class should be able 
> to translate between the different possible representations of links (Gauss 
> codes, 3d curves, braid closure...) and compute some of their invariants 
> (the usual polynomials, Seifert forms, fundamental groups...). It should 
> also produce pictures of knot diagrams and 3d representations of the 
> knot/link. Some (or most) of this features can be either written from 
> scratch, or just wrap external code (like the mentioned SnapPy).

perhaps one can try to incorporate parts of knotscape into Sage.
Well, it's kind of old, but still works:
https://github.com/dimpase/knotscap
(incidentally, a colleague wanted to use knotscape on a modern Linux
system, so I did these small fixes for him)


>
> Another idea, closely related to the previous one, is to write a javascript 
> editor for knots and links, following what knotplot [1] does. This can be 
> part of the same project or a separated one, if someone else writes the 
> backend (although i think that it should be possible to write the editor 
> and a simple backend in a single gsoc project, but that can be discussed). 
> An important part of this editor would be the algorithm for dynamically 
> relaxing the link. In particular, such an algorithm is explained in chapter 
> 7 of Scharein's thesis [1].
>
> [1] http://www.knotplot.com/thesis/thesis.html
>

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Re: [sage-devel] Re: Sage accepted for GSoC 2014

2014-02-25 Thread Amit Jamadagni
I have been going through the implementation Knot Atlas, as per my
understanding they have stored the knots in a table and have inputted it to
get various results, I would like to know whether we will be using tables
to input or any other way to input. I have seen through Vogel's algorithm
 which takes in the oriented gauss code and ends up giving out the braid
word [1] from which we can construct the knot(as it is closed braid) and
from the braid word we can calculate the Alexander polynomial from the
Burau's representation(which is currently implemented in braid in Sage) (I
have heard is not true for strings greater than 5). I have been reading
through [2] which mentions how to calculate Seifert matrix from a braid
representation which can be again used to represent knots. I have been
searching for algorithms which would relate the Seifert matrix and various
invariants. It would be really helpful if I could get more reference to the
algorithms that could be implemented. I have just started the
implementation details mentioned in [3].

[1] http://magma.maths.usyd.edu.au/~danr/site/talks/20070531.pdf
[2] http://www.maths.ed.ac.uk/~jcollins/SeifertMatrix/SeifertMatrix.pdf
[3] http://www.layer8.co.uk/maths/braids/braid-user-documentation.html

On Tue, Feb 25, 2014 at 7:16 PM, kcrisman  wrote:

>
>>
>> [2] http://legacy.earlham.edu/~peters/knotlink.htm#software
>>
>>
> *"June 2, 2004*. Unfortunately I no longer have time to update *Knots on
> the Web*. I know it conntains many dead links and omits many good, new
> sites. "
>
> And my understanding is that the Knot Atlas
> http://katlas.math.toronto.edu/wiki/Main_Page and the Mathematica package
> creating it is the state of the art.  Does SnapPy now really have all that
> combinatorial stuff?  I think that at the very least a good wrapper
> allowing for use of *any* robust backend for knots would be a great
> contribution to Sage.  mmarco seems to have a good sense of what would
> actually be needed to do this.  It's definitely a significant hole in Sage.
> - one might even wonder whether the authors of the Mma package would be
> willing to license their package in such a way that the algorithms for
> computing various invariants etc. could be used/{P,C}ythonized in Sage, if
> some people know them http://katlas.math.toronto.edu/wiki/Acknowledgement
>
> --
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Re: [sage-devel] Re: Sage accepted for GSoC 2014

2014-02-25 Thread kcrisman

>
>
>
> [2] http://legacy.earlham.edu/~peters/knotlink.htm#software 
>
>
*"June 2, 2004*. Unfortunately I no longer have time to update *Knots on 
the Web*. I know it conntains many dead links and omits many good, new 
sites. "

And my understanding is that the Knot 
Atlas http://katlas.math.toronto.edu/wiki/Main_Page and the Mathematica 
package creating it is the state of the art.  Does SnapPy now really have 
all that combinatorial stuff?  I think that at the very least a good 
wrapper allowing for use of *any* robust backend for knots would be a great 
contribution to Sage.  mmarco seems to have a good sense of what would 
actually be needed to do this.  It's definitely a significant hole in Sage. 
- one might even wonder whether the authors of the Mma package would be 
willing to license their package in such a way that the algorithms for 
computing various invariants etc. could be used/{P,C}ythonized in Sage, if 
some people know them http://katlas.math.toronto.edu/wiki/Acknowledgement

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[sage-devel] Re: Sage accepted for GSoC 2014

2014-02-25 Thread mmarco
I would be happy to mentor a student in a knot theory related project in 
sage. I had mainly two ideas:

First idea is to write a class for knots/links. This class should be able 
to translate between the different possible representations of links (Gauss 
codes, 3d curves, braid closure...) and compute some of their invariants 
(the usual polynomials, Seifert forms, fundamental groups...). It should 
also produce pictures of knot diagrams and 3d representations of the 
knot/link. Some (or most) of this features can be either written from 
scratch, or just wrap external code (like the mentioned SnapPy).

Another idea, closely related to the previous one, is to write a javascript 
editor for knots and links, following what knotplot [1] does. This can be 
part of the same project or a separated one, if someone else writes the 
backend (although i think that it should be possible to write the editor 
and a simple backend in a single gsoc project, but that can be discussed). 
An important part of this editor would be the algorithm for dynamically 
relaxing the link. In particular, such an algorithm is explained in chapter 
7 of Scharein's thesis [1].

[1] http://www.knotplot.com/thesis/thesis.html

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Re: [sage-devel] Re: Sage accepted for GSoC 2014

2014-02-25 Thread Amit Jamadagni
Hello Volker,
   Thanks for the reply. As I have posted in the recent
threads, I would like to discuss this project and have created a thread for
the same on the sage-gsoc group. I hope you've had a look at it (
https://groups.google.com/forum/#!topic/sage-gsoc/tb2O7zEoUx0) , it would
be really great if you could comment on it as it would provide me with an
idea of the implementation that can be done. Thanks.


On Tue, Feb 25, 2014 at 4:06 PM, Volker Braun  wrote:

> We certainly could to use some of the SnapPy parts, like look at the
> Tcl/Tk link editor. But thats not going to integrate into the notebook.
> Also, link plots could look imho better. Apart from the GUI side, we need
> something that we can interface with more research-y codes written in GAP
> or Singular which SnapPy can't do.
>
>
>
> On Tuesday, February 25, 2014 8:35:39 AM UTC+1, vdelecroix wrote:
>>
>> There are already plenty of math software for knot theory. One very
>> active is SnapPy [1]
>>
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Re: [sage-devel] Re: Sage accepted for GSoC 2014

2014-02-25 Thread Volker Braun
We certainly could to use some of the SnapPy parts, like look at the Tcl/Tk 
link editor. But thats not going to integrate into the notebook. Also, link 
plots could look imho better. Apart from the GUI side, we need something 
that we can interface with more research-y codes written in GAP or Singular 
which SnapPy can't do.

 

On Tuesday, February 25, 2014 8:35:39 AM UTC+1, vdelecroix wrote:
>
> There are already plenty of math software for knot theory. One very 
> active is SnapPy [1] 
>

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Re: [sage-devel] Re: Sage accepted for GSoC 2014

2014-02-25 Thread Amit Jamadagni
Hello Vincent,
   Thanks for the reply. I wanted to work on the implementation as
it was mentioned in the ideas page(
https://docs.google.com/document/d/15v7lXZR1U4H2pT21d2fyPduYGb74JAFjkXJ6CWYmYfw/pub).
 I have introduced myself and posted about the same on the sage-gsoc google
group. I wanted to know whether I need to forward the discussion to the
possible mentors mentioned on the ideas page or whether it was sufficient
just to post on that group. Coming back to the implementation I will look
through SnapPy and its integration with Sage and get back in touch with you
as soon as possible. Thanks for all the help and guidance.

Amit.


On Tue, Feb 25, 2014 at 1:05 PM, Vincent Delecroix <
20100.delecr...@gmail.com> wrote:

> Hello Amit,
>
> > I am a student and I would like to participate in SoC. I have
> > already posted about my interest on working about the implementation of
> > Knot Theory. Is it necessary that the message be forwarded to mentors or
> > any other mailing list other than this one ??  Thanks.
>
> There are already plenty of math software for knot theory. One very
> active is SnapPy [1] but you can find several lists of softwares on
> the web such as [2]. SnapPy is licensed GPLv2+ so it should be
> compatible with Sage. SnapPy is already packaged for Sage [3] but the
> integration could be smoother (in particular the package might be
> available from sagemath.org website).
> If you are interested in knot theory, one option is to contact authors
> of SnapPy (Marc Culler and Nathan Dunfield from Chicago) and see if
> they can mentor you for a Sage related project. You can mention my
> name to them and if needed I could also possibly do part of the
> mentoring.
> In any case do not start from scratch implementing knots in Sage. It
> would be a waste of time.
>
> All best,
> Vincent Delecroix (from France)
>
> [1] http://www.math.uic.edu/t3m/SnapPy/
> [2] http://legacy.earlham.edu/~peters/knotlink.htm#software
> [3] http://www.math.uic.edu/t3m/SnapPy/installing.html#sage
>
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Re: [sage-devel] Re: Sage accepted for GSoC 2014

2014-02-24 Thread Vincent Delecroix
Hello Amit,

> I am a student and I would like to participate in SoC. I have
> already posted about my interest on working about the implementation of
> Knot Theory. Is it necessary that the message be forwarded to mentors or
> any other mailing list other than this one ??  Thanks.

There are already plenty of math software for knot theory. One very
active is SnapPy [1] but you can find several lists of softwares on
the web such as [2]. SnapPy is licensed GPLv2+ so it should be
compatible with Sage. SnapPy is already packaged for Sage [3] but the
integration could be smoother (in particular the package might be
available from sagemath.org website).
If you are interested in knot theory, one option is to contact authors
of SnapPy (Marc Culler and Nathan Dunfield from Chicago) and see if
they can mentor you for a Sage related project. You can mention my
name to them and if needed I could also possibly do part of the
mentoring.
In any case do not start from scratch implementing knots in Sage. It
would be a waste of time.

All best,
Vincent Delecroix (from France)

[1] http://www.math.uic.edu/t3m/SnapPy/
[2] http://legacy.earlham.edu/~peters/knotlink.htm#software
[3] http://www.math.uic.edu/t3m/SnapPy/installing.html#sage

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Re: [sage-devel] Re: Sage accepted for GSoC 2014

2014-02-24 Thread Amit Jamadagni
Hello,
I am a student and I would like to participate in SoC. I have
already posted about my interest on working about the implementation of
Knot Theory. Is it necessary that the message be forwarded to mentors or
any other mailing list other than this one ??  Thanks.


On Tue, Feb 25, 2014 at 3:18 AM, William Stein  wrote:

> Somebody needs to update this: http://wiki.sagemath.org/GSoC
>
> On Mon, Feb 24, 2014 at 11:13 AM, Harald Schilly
>  wrote:
> > No. First we need the proposals and we evaluate and rank them. This
> > means, everyone discusses them, gives them a number from 0 to 10, and
> > we set their state to "ok" (or however it is called) or invalid.
> > Then I am, in my role as administrator, tell google melange two
> > numbers: minimum number of how many projects we really want, and a
> > maximum number. After that, we'll get green lights projects sorted by
> > rank and if necessary, there are additional rounds of "deduplication"
> > and so on.
> >
> > harald
> >
> >
> > On Mon, Feb 24, 2014 at 8:06 PM, mmarco  wrote:
> >> Good to hear. Do we already know how many students will be assigned?
> >>
> >> --
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>
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Re: [sage-devel] Re: Sage accepted for GSoC 2014

2014-02-24 Thread William Stein
Somebody needs to update this: http://wiki.sagemath.org/GSoC

On Mon, Feb 24, 2014 at 11:13 AM, Harald Schilly
 wrote:
> No. First we need the proposals and we evaluate and rank them. This
> means, everyone discusses them, gives them a number from 0 to 10, and
> we set their state to "ok" (or however it is called) or invalid.
> Then I am, in my role as administrator, tell google melange two
> numbers: minimum number of how many projects we really want, and a
> maximum number. After that, we'll get green lights projects sorted by
> rank and if necessary, there are additional rounds of "deduplication"
> and so on.
>
> harald
>
>
> On Mon, Feb 24, 2014 at 8:06 PM, mmarco  wrote:
>> Good to hear. Do we already know how many students will be assigned?
>>
>> --
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>
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-- 
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Professor of Mathematics
University of Washington
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Re: [sage-devel] Re: Sage accepted for GSoC 2014

2014-02-24 Thread Harald Schilly
No. First we need the proposals and we evaluate and rank them. This
means, everyone discusses them, gives them a number from 0 to 10, and
we set their state to "ok" (or however it is called) or invalid.
Then I am, in my role as administrator, tell google melange two
numbers: minimum number of how many projects we really want, and a
maximum number. After that, we'll get green lights projects sorted by
rank and if necessary, there are additional rounds of "deduplication"
and so on.

harald


On Mon, Feb 24, 2014 at 8:06 PM, mmarco  wrote:
> Good to hear. Do we already know how many students will be assigned?
>
> --
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[sage-devel] Re: Sage accepted for GSoC 2014

2014-02-24 Thread mmarco
Good to hear. Do we already know how many students will be assigned?

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