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[Staden-package] FASD project: Online survey launched

From: <benno.luthiger@id...> - 2004-05-25 09:49

Dear Open Source developer

I am doing a research project on "Fun and Software Development" in which I kindly invite you to participate.
You will find the online survey under http://fasd.ethz.ch/qsf/. The questionnaire consists of 53 questions and you will need about 15 minutes to complete it.

With the FASD project (Fun and Software Development) we want to define the motivational significance of fun when software developers decide to engage in Open Source projects. What is special about our research project is that a similar survey is planned with software developers in commercial firms. This procedure allows the immediate comparison between the involved individuals and the conditions of production of these two development models. Thus we hope to obtain substantial new insights to the phenomenon of Open Source Development.


With many thanks for your participation,
Benno Luthiger


PS:
The results of the survey will be published under http://www.isu.unizh.ch/fuehrung/blprojects/FASD/.
We have set up the mailing list fasd@... for this study. Please see http://fasd.ethz.ch/qsf/mailinglist_en.html for registration to this mailing list.

_______________________________________________________________________

Benno Luthiger
Swiss Federal Institute of Technology Zurich
8092 Zurich

Mail: benno.luthiger(at)id.ethz.ch
_______________________________________________________________________

RE: [Staden-package] Use of ABI 3730 KB-basecalled traces in Pregap4?

From: Edith Schlagenhauf <ediths@bo...> - 2004-05-12 07:39

I already tried to use the .scf files produced by the
3730 Sequencing Analysis software, v5.1 - but there appear
to be no quality values output ...
And the phd.1 files output do contain incomplete headers..
Applied Biosystems wants to fix the bugs.

But I am still using Staden 2002.0 version, thus : first
thing to do: update to v. 1.4.0/1 package release ;-)


******************************************
Dr Edith Schlagenhauf
Bioinformatics
Institute of Plant Biology
University of Zurich

e-mail: ediths AT botinst DOT unizh DOT ch
******************************************

On Tue, 11 May 2004, Cook, Malcolm wrote:

> Chiming in!
>
> Trev version 1.8b1 for windows, part of "Version-2003.0-beta" does not
> display them when you turn on "Disply confidence".
>
> Attached is a sample .ab1 file.
>
> I think the 3730 data colleciton software can be configured to
> optionally generate a .scf file in addition to the .ab1 (as well as a
> ".phd.1" file such as is liked by phrap), and the .scf file should open
> in trev and display the confidence scores.  I'm checking on this...
>
> Malcolm Cook - mec@... - 816-926-4449
> Database Applications Manager - Bioinformatics
> Stowers Institute for Medical Research - Kansas City, MO  USA
>
>
>
>
>
>
> >-----Original Message-----
> >From: James Bonfield [mailto:jkb@...]
> >Sent: Tuesday, May 11, 2004 11:25 AM
> >To: Edith Schlagenhauf
> >Cc: staden-package@...
> >Subject: Re: [Staden-package] Use of ABI 3730 KB-basecalled
> >traces in Pregap4?
> >
> >
> >On Tue, May 11, 2004 at 05:16:15PM +0200, Edith Schlagenhauf wrote:
> >> I tried to use KB-basecalled traces from an ABI 3730
> >> sequencer directly in Pregap4, but "Trace Format
> >> Conversion" obviously does not know about quality values
> >> present in the AB1 file. How do you proceed to
> >> process such data in Pregap4 ?
> >
> >Pregap4 is simply using convert_trace to create SCF or ZTR files from
> >AB1 files. convert_trace in turn uses io_lib.
> >
> >The latest io_lib code does support the PCON field of AB1 files. Is it
> >this record that KB is using to store confidence values in? PCON was,
> >I think, initially added to store phred confidence values when people
> >started asking for a way to upload phred data into BioLIMS.
> >
> >I think that the PCON support should be in the 1.4.0/1 package
> >release.
> >
> >The easiest way to verify this is simply to use trev to view the AB1
> >file to see if the confidence values are there. If so then pregap4
> >should also be working.
> >
> >Could you please email me an example KB basecalled AB1 file so I can
> >verify the latest code works?
> >
> >James
> >
> >--
> >James Bonfield (jkb@...)
> >A Staden Package developer: https://sourceforge.net/projects/staden/
> >
> >
> >-------------------------------------------------------
> >This SF.Net email is sponsored by Sleepycat Software
> >Learn developer strategies Cisco, Motorola, Ericsson & Lucent use to
> >deliver higher performing products faster, at low TCO.
> >http://www.sleepycat.com/telcomwpreg.php?From=osdnemail3
> >_______________________________________________
> >Staden-package mailing list
> >Staden-package@...
> >https://lists.sourceforge.net/lists/listinfo/staden-package
> >
>

RE: [Staden-package] Use of ABI 3730 KB-basecalled traces in Pregap4?

From: Cook, Malcolm <MEC@St...> - 2004-05-11 18:15

Attachments: G-5-T7_A12.ab1

Chiming in!

Trev version 1.8b1 for windows, part of "Version-2003.0-beta" does not
display them when you turn on "Disply confidence".

Attached is a sample .ab1 file.

I think the 3730 data colleciton software can be configured to
optionally generate a .scf file in addition to the .ab1 (as well as a
".phd.1" file such as is liked by phrap), and the .scf file should open
in trev and display the confidence scores.  I'm checking on this...

Malcolm Cook - mec@... - 816-926-4449
Database Applications Manager - Bioinformatics
Stowers Institute for Medical Research - Kansas City, MO  USA=20






>-----Original Message-----
>From: James Bonfield [mailto:jkb@...
>Sent: Tuesday, May 11, 2004 11:25 AM
>To: Edith Schlagenhauf
>Cc: staden-package@...
>Subject: Re: [Staden-package] Use of ABI 3730 KB-basecalled=20
>traces in Pregap4?
>
>
>On Tue, May 11, 2004 at 05:16:15PM +0200, Edith Schlagenhauf wrote:
>> I tried to use KB-basecalled traces from an ABI 3730
>> sequencer directly in Pregap4, but "Trace Format
>> Conversion" obviously does not know about quality values
>> present in the AB1 file. How do you proceed to
>> process such data in Pregap4 ?
>
>Pregap4 is simply using convert_trace to create SCF or ZTR files from
>AB1 files. convert_trace in turn uses io_lib.
>
>The latest io_lib code does support the PCON field of AB1 files. Is it
>this record that KB is using to store confidence values in? PCON was,
>I think, initially added to store phred confidence values when people
>started asking for a way to upload phred data into BioLIMS.
>
>I think that the PCON support should be in the 1.4.0/1 package
>release.
>
>The easiest way to verify this is simply to use trev to view the AB1
>file to see if the confidence values are there. If so then pregap4
>should also be working.
>
>Could you please email me an example KB basecalled AB1 file so I can
>verify the latest code works?
>
>James
>
>--=20
>James Bonfield (jkb@...)
>A Staden Package developer: https://sourceforge.net/projects/staden/
>
>
>-------------------------------------------------------
>This SF.Net email is sponsored by Sleepycat Software
>Learn developer strategies Cisco, Motorola, Ericsson & Lucent use to=20
>deliver higher performing products faster, at low TCO.
>http://www.sleepycat.com/telcomwpreg.php?From=3Dosdnemail3
>_______________________________________________
>Staden-package mailing list
>Staden-package@...
>https://lists.sourceforge.net/lists/listinfo/staden-package
>

RE: [Staden-package] Use of ABI 3730 KB-basecalled traces in Pregap4?

From: Cook, Malcolm <MEC@St...> - 2004-05-12 15:16

James & Edith,

I checked, and, as far as I can tell, the scf files when displayed in
trev 1.8b1 for windows do NOT show quality scores either.

Edith,

If it helps your purpose, in the mean time I know of one other viewer
that will open ab1 files and display the quality scores.  It is free.
It is Finch TV - http://www.geospiza.com/finchtv/download/index.html

Cheers,

Malcolm

>-----Original Message-----
>From: Cook, Malcolm=20
>Sent: Tuesday, May 11, 2004 1:15 PM
>To: James Bonfield; Edith Schlagenhauf
>Cc: staden-package@...
>Subject: RE: [Staden-package] Use of ABI 3730 KB-basecalled=20
>traces in Pregap4?
>
>
>Chiming in!
>
>Trev version 1.8b1 for windows, part of "Version-2003.0-beta" does not
>display them when you turn on "Disply confidence".
>
>Attached is a sample .ab1 file.
>
>I think the 3730 data colleciton software can be configured to
>optionally generate a .scf file in addition to the .ab1 (as well as a
>".phd.1" file such as is liked by phrap), and the .scf file should open
>in trev and display the confidence scores.  I'm checking on this...
>
>Malcolm Cook - mec@... - 816-926-4449
>Database Applications Manager - Bioinformatics
>Stowers Institute for Medical Research - Kansas City, MO  USA=20
>
>
>
>
>
>
>>-----Original Message-----
>>From: James Bonfield [mailto:jkb@...
>>Sent: Tuesday, May 11, 2004 11:25 AM
>>To: Edith Schlagenhauf
>>Cc: staden-package@...
>>Subject: Re: [Staden-package] Use of ABI 3730 KB-basecalled=20
>>traces in Pregap4?
>>
>>
>>On Tue, May 11, 2004 at 05:16:15PM +0200, Edith Schlagenhauf wrote:
>>> I tried to use KB-basecalled traces from an ABI 3730
>>> sequencer directly in Pregap4, but "Trace Format
>>> Conversion" obviously does not know about quality values
>>> present in the AB1 file. How do you proceed to
>>> process such data in Pregap4 ?
>>
>>Pregap4 is simply using convert_trace to create SCF or ZTR files from
>>AB1 files. convert_trace in turn uses io_lib.
>>
>>The latest io_lib code does support the PCON field of AB1 files. Is it
>>this record that KB is using to store confidence values in? PCON was,
>>I think, initially added to store phred confidence values when people
>>started asking for a way to upload phred data into BioLIMS.
>>
>>I think that the PCON support should be in the 1.4.0/1 package
>>release.
>>
>>The easiest way to verify this is simply to use trev to view the AB1
>>file to see if the confidence values are there. If so then pregap4
>>should also be working.
>>
>>Could you please email me an example KB basecalled AB1 file so I can
>>verify the latest code works?
>>
>>James
>>
>>--=20
>>James Bonfield (jkb@...)
>>A Staden Package developer: https://sourceforge.net/projects/staden/
>>
>>
>>-------------------------------------------------------
>>This SF.Net email is sponsored by Sleepycat Software
>>Learn developer strategies Cisco, Motorola, Ericsson & Lucent use to=20
>>deliver higher performing products faster, at low TCO.
>>http://www.sleepycat.com/telcomwpreg.php?From=3Dosdnemail3
>>_______________________________________________
>>Staden-package mailing list
>>Staden-package@...
>>https://lists.sourceforge.net/lists/listinfo/staden-package
>>
>

Re: [Staden-package] Use of ABI 3730 KB-basecalled traces in Pregap4?

From: James Bonfield <jkb@sa...> - 2004-05-12 15:47

On Wed, May 12, 2004 at 10:16:05AM -0500, Cook, Malcolm wrote:
> I checked, and, as far as I can tell, the scf files when displayed in
> trev 1.8b1 for windows do NOT show quality scores either.

I just checked the rel-1.4 release on linux and it DOES show the
confidence values.

For windows I haven't made the latest release available yet (although
at last I have access to a build environment that would allow me to
start on this).

So the solution to this is just for now to use an up to date unix
version of Trev.

> If it helps your purpose, in the mean time I know of one other viewer
> that will open ab1 files and display the quality scores.  It is free.
> It is Finch TV - http://www.geospiza.com/finchtv/download/index.html

Nice program.

On a similar vane, if you use MacOS X check out 4Peaks
(http://www.mekentosj.com/4peaks/index.html). It's probably the "Bee's
Knees" of trace viewers!

James

-- 
James Bonfield (jkb@...)
A Staden Package developer: https://sourceforge.net/projects/staden/

RE: [Staden-package] Use of ABI 3730 KB-basecalled traces in Pregap4?

From: Cook, Malcolm <MEC@St...> - 2004-05-12 15:52

James,

>I just checked the rel-1.4 release on linux and it DOES show the
>confidence values.

Excellent news James.  Thanks for checking!

>For windows I haven't made the latest release available yet (although
>at last I have access to a build environment that would allow me to
>start on this).

Great too.  I have many users captive to windows who will benefit when
this happens.

>On a similar vane, if you use MacOS X check out 4Peaks
>(http://www.mekentosj.com/4peaks/index.html). It's probably the "Bee's
>Knees" of trace viewers!

Too bad, I no longer work with Macs much at all....

Regards,

Malcolm

[Staden-package] Use of ABI 3730 KB-basecalled traces in Pregap4?

From: Edith Schlagenhauf <ediths@bo...> - 2004-05-11 15:16

Dear all,

I tried to use KB-basecalled traces from an ABI 3730
sequencer directly in Pregap4, but "Trace Format
Conversion" obviously does not know about quality values
present in the AB1 file. How do you proceed to
process such data in Pregap4 ?

Thanks for inspirations,
Edith


******************************************
Dr Edith Schlagenhauf
Bioinformatics
University of Zurich

e-mail: ediths AT botinst DOT unizh DOT ch
******************************************

Re: [Staden-package] Use of ABI 3730 KB-basecalled traces in Pregap4?

From: James Bonfield <jkb@sa...> - 2004-05-11 16:25

On Tue, May 11, 2004 at 05:16:15PM +0200, Edith Schlagenhauf wrote:
> I tried to use KB-basecalled traces from an ABI 3730
> sequencer directly in Pregap4, but "Trace Format
> Conversion" obviously does not know about quality values
> present in the AB1 file. How do you proceed to
> process such data in Pregap4 ?

Pregap4 is simply using convert_trace to create SCF or ZTR files from
AB1 files. convert_trace in turn uses io_lib.

The latest io_lib code does support the PCON field of AB1 files. Is it
this record that KB is using to store confidence values in? PCON was,
I think, initially added to store phred confidence values when people
started asking for a way to upload phred data into BioLIMS.

I think that the PCON support should be in the 1.4.0/1 package
release.

The easiest way to verify this is simply to use trev to view the AB1
file to see if the confidence values are there. If so then pregap4
should also be working.

Could you please email me an example KB basecalled AB1 file so I can
verify the latest code works?

James

-- 
James Bonfield (jkb@...)
A Staden Package developer: https://sourceforge.net/projects/staden/