presents, you say?

On 06/28/2010 12:58 PM, Kenny Billiau wrote:

I bet he gets loads of presents this way ..

On Mon, 28 Jun 2010, Frederik Delaere wrote:

born the 24th of july 1984 ?

Kenny Billiau wrote:

and don't you just love their very descriptive email address .. ;)

On Mon, 28 Jun 2010, Frederik Delaere wrote:

looks like the average help request mail overhere :)

Michiel Van Bel wrote:

*sigh*
sometimes I really want to tell those guys to
a) follow a decent english course
b) read the fucking manual

I mean, it's not that difficult to read your email again before you
send
it, and make sure it makes sense :-(

---------------------------- Original Message
----------------------------
Subject: Re:Re: Fw: A PHD student using splice machine
From:    ¿µÑ©æ¯ <kxj19840724@126.com>
Date:    Sun, June 27, 2010 4:14 am
To:      "Michiel Van Bel" <michiel.vanbel@psb.vib-ugent.be>
--------------------------------------------------------------------------

Dear Michiel
       Thanks for your help!
       I have tried to predict my test file using the software but the
annotation file can be downloaded,why?

      Best regards!

     Xuejiao

ok,
the software available on the website is only trained for Arabidopsis
and Human.
So you can only use a test-file (in fasta format). The
output-format is
described here:
http://bioinformatics.psb.ugent.be/webtools/splicemachine/help/

In order to train splicemachine yourself, you'll have to use the
offline
installation (see attachment).
However, as I didn't write the software, I do not think I can really
help you any further with any questions considering training
splicemachine yourself. Please have a look at the pdf-files
included in
the attachment, for any further instructions.

Michiel

¿µÑ©æ¯ wrote:

Hi Michieal
Thanks for your reply!
Here I want to know how to run the software.To the inputing file, how
to distinguish the training file and the testing file?or the all the
data should be in one file?Then how to distinguish the true or false
sites?
Thanks a lot!
Regards!
Xuejiao

Hi Kang,
you can run the splicemachine software at this location:
http://bioinformatics.psb.ugent.be/webtools/splicemachine/

Just copy-paste the sequences in fasta format into the
text-field, and
press the "run splicemachine" button.

kind regards,
Michiel

Yves Van De Peer wrote:

------------------------------------------------------------------------

*From*: ¿µÑ©æ¯ <kxj19840724@126.com>
*To*: yves.vandepeer@psb.vib-ugent.be
<yves.vandepeer@psb.vib-ugent.be>
*Sent*: Fri Jun 25 08:31:52 2010
*Subject*: A PHD student using splice machine

Dear Professor
        I'm a PHD student doing research in splice sites prediction
and I have read your article"Splice Machine: predicting splice
sites
from high-dimensional local context representations". Now I want
to do
some comparisons on NN269 acceptor datasets, but I don't know
how to
use the software(how to do prediction). Would you like to tell
me the
details?
       Best wishes to you and your family!
       Thanks a lot!

       Yours sincerely
       Kang xuejiao

--
==================================================================
Michiel Van Bel
PhD student
Tel:+32 (0)9 331 36 95                        fax:+32 (0)9 3313809
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927, 9052 Gent, BELGIUM
mibel@psb.vib-ugent.be

http://www.psb.vib-ugent.be

http://bioinformatics.psb.ugent.be
==================================================================

--
==================================================================
Michiel Van Bel
PhD student
Tel:+32 (0)9 331 36 95                        fax:+32 (0)9 3313809
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927, 9052 Gent, BELGIUM
mibel@psb.vib-ugent.be
http://www.psb.vib-ugent.be
http://bioinformatics.psb.ugent.be
==================================================================

------------------------------------------------------------------------

Dear Michiel
       Thanks for your help!
       I have tried to predict my test file using the software but the
annotation file can be downloaded,why?

      Best regards!

     Xuejiao

ok,
the software available on the website is only trained for Arabidopsis
and Human.
So you can only use a test-file (in fasta format). The
output-format is
described here:
http://bioinformatics.psb.ugent.be/webtools/splicemachine/help/

In order to train splicemachine yourself, you'll have to use the
offline
installation (see attachment).
However, as I didn't write the software, I do not think I can really
help you any further with any questions considering training
splicemachine yourself. Please have a look at the pdf-files
included in
the attachment, for any further instructions.

Michiel

¿µÑ©æ¯ wrote:

Hi Michieal
Thanks for your reply!
Here I want to know how to run the software.To the inputing file, how
to distinguish the training file and the testing file?or the all the
data should be in one file?Then how to distinguish the true or false
sites?
Thanks a lot!
Regards!
Xuejiao

Hi Kang,
you can run the splicemachine software at this location:
http://bioinformatics.psb.ugent.be/webtools/splicemachine/

Just copy-paste the sequences in fasta format into the
text-field, and
press the "run splicemachine" button.

kind regards,
Michiel

Yves Van De Peer wrote:

------------------------------------------------------------------------

*From*: ¿µÑ©æ¯ <kxj19840724@126.com>
*To*: yves.vandepeer@psb.vib-ugent.be
<yves.vandepeer@psb.vib-ugent.be>
*Sent*: Fri Jun 25 08:31:52 2010
*Subject*: A PHD student using splice machine

Dear Professor
        I'm a PHD student doing research in splice sites prediction
and I have read your article"Splice Machine: predicting splice
sites
from high-dimensional local context representations". Now I want
to do
some comparisons on NN269 acceptor datasets, but I don't know
how to
use the software(how to do prediction). Would you like to tell
me the
details?
       Best wishes to you and your family!
       Thanks a lot!

       Yours sincerely
       Kang xuejiao

--
==================================================================
Michiel Van Bel
PhD student
Tel:+32 (0)9 331 36 95                        fax:+32 (0)9 3313809
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927, 9052 Gent, BELGIUM
mibel@psb.vib-ugent.be
http://www.psb.vib-ugent.be
http://bioinformatics.psb.ugent.be
==================================================================

--
==================================================================
Michiel Van Bel
PhD student
Tel:+32 (0)9 331 36 95                        fax:+32 (0)9 3313809
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927, 9052 Gent, BELGIUM
mibel@psb.vib-ugent.be
http://www.psb.vib-ugent.be
http://bioinformatics.psb.ugent.be
==================================================================

------------------------------------------------------------------------

_______________________________________________
Binari Implicitly Neglects All Recursive Iterations
https://maillist.psb.ugent.be/mailman/listinfo/binari

--
======================================================================
Kenny Billiau                          Bioinformatics Group / GoFORSYS
Scientific Programmer
+49 331 567 8626                             billiau@mpimp-golm.mpg.de
Max Planck Institute for Molecular Plant Physiology
Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
http://bioinformatics.mpimp-golm.mpg.de         http://www.goforsys.de
======================================================================
------------------------------------------------------------------------

_______________________________________________
Binari Implicitly Neglects All Recursive Iterations
https://maillist.psb.ugent.be/mailman/listinfo/binari

--
==================================================================
Frederik Delaere

Tel:+32 (0)9 331 38 14                        fax:+32 (0)9 3313809
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927, 9052 Gent, BELGIUM
frlae@psb.vib-ugent.be                 http://www.psb.vib-ugent.be
==================================================================

_______________________________________________
Binari Implicitly Neglects All Recursive Iterations
https://maillist.psb.ugent.be/mailman/listinfo/binari

--
======================================================================
Kenny Billiau                          Bioinformatics Group / GoFORSYS
Scientific Programmer
+49 331 567 8626                             billiau@mpimp-golm.mpg.de
Max Planck Institute for Molecular Plant Physiology
Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
http://bioinformatics.mpimp-golm.mpg.de         http://www.goforsys.de
======================================================================
_______________________________________________
Binari Implicitly Neglects All Recursive Iterations
https://maillist.psb.ugent.be/mailman/listinfo/binari
  