kbradnam@mac.com | 24 Jan 2008 17:13
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Acedb on OS X 10.5 (Leopard)


The 4.9.39 binaries of xace and tace will work on Leopard...with a
little help.

You need to also install glib and gtk+. In the past I have done this
by using the fink project (http://www.finkproject.org/). However, the
version of glib available under fink doesn't meet the specifications
of what acedb needs. So, I tried installing MacPorts (http://
www.macports.org/) which has a similar raison d'etre to fink, and this
has a later version of glib.

So download MacPorts, use it to install glib, gtk+ and readline, and
then make one final tweak. Acedb will look in /usr/local/lib whereas
MacPorts installs to /opt/local/lib. So I just created a sym link at /
usr/local/lib to point to /opt/local/lib.

Regards,

Keith

Ed Griffiths | 15 Nov 2007 10:48
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Bionet public archives and privacy

All,

Please read the below from Don Gilbert who supervises/coordinates much of the 
bionet archives.

I'm not aware of any issues for acedb but if you have concerns you should 
probably contact me directly in the first instance.

Ed
-- 
  ------------------------------------------------------------------------
| Ed Griffiths, Acedb development, Informatics Group,                    |
|  The Morgan Building, Sanger Institute, Wellcome Trust Genome Campus   |
|  Hinxton, Cambridge CB10 1HH                                           |
|                                                                        |
| email: edgrif <at> sanger.ac.uk  Tel: +44-1223-496844  Fax: +44-1223-494919 |
  ------------------------------------------------------------------------

---------- Forwarded message ----------
Date: Tue, 13 Nov 2007 17:18:49 -0500 (EST)
From: Don Gilbert <gilbertd <at> cricket.bio.indiana.edu>
To: biomail <at> magpie.bio.indiana.edu
Subject: [Biomail Site List] Update on Bionet public archives and privacy
     	concerns

Dear Bionet moderators,

As some contributors change their minds or learn after the fact
that any public discussions become Google'able and expose their
messages to searches by name, I and likely some of you, get
(Continue reading)

Aleksei Petrov | 22 Aug 2007 18:05
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to Jhon: 139 error

Hello Jhon,

I got error message "Error status = 139" while loading data into
acedb.  Do you know what that means?





--------------------------------
--------------------------------
Best Regards,
Alveksei
<a href="http://www.diabetes.pocket-book.com/">diabetes weblog</a>

<div><p>Hello Jhon,<br><br>I got error message "Error status = 139" while loading data into<br>acedb.&nbsp; Do you know what that means?<br><br><br><br><br><br>--------------------------------<br>--------------------------------
<br>Best Regards,<br>Alveksei<br>&lt;a href="<a href="http://www.diabetes.pocket-book.com/">http://www.diabetes.pocket-book.com/</a>"&gt;diabetes weblog&lt;/a&gt;<br><br></p></div>
Aleksei Petrov | 22 Aug 2007 17:57
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to Jhon: 139 error

Hello Jhon,

I got error message "Error status = 139" while loading data into
acedb.  Do you know what that means?


--------------------------------
--------------------------------
Best Regards,
Alveksei
<a href="http://www.diabetes.pocket-book.com/">diabetes weblog</a>

<div><p>Hello Jhon,<br><br>I got error message "Error status = 139" while loading data into<br>acedb.&nbsp; Do you know what that means?<br><br><br>--------------------------------<br>--------------------------------<br>Best Regards,
<br>Alveksei<br>&lt;a href="<a href="http://www.diabetes.pocket-book.com/">http://www.diabetes.pocket-book.com/</a>"&gt;diabetes weblog&lt;/a&gt;</p></div>
Jean Thierry-Mieg | 14 Mar 2007 17:28
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Re: aql error 810, Inconsistent value types


>What does this error message mean?
>
>// AQL error 810 around: 'l, m, p from s in'
>//                              ^
>// Inconsistent value types in table column 3
>// Value type was 'g' and now the field evaluates to type 'f' in row 19822
>
>What are value types g and f?
>
f is type float
g is type tag

it means that in m[2] you had something heterogeneous
the only way i see to produce that is that the model
allowed either float or tag at this position

either you did a read-model during the lifetime of the database
this does not erase the data, the dumper still works
the purpose of this is that we do not lose data in acedb
by reading a wrong model, we just loose access via queries
(direct query, table maker, aql, aceperl)
but the dumper survives

or the schema is complex and you should select on m[1]
to be sure that m[2] is a float

Maybe te schema is

?Sequence Map #map_info

#map_info Position float
          Neighbours Left ?Sequence
                     Right ?Sequence

                  
.ace file:

Sequence s1
Map 2 Position 3.2

Sequence s2
Map 4 Neighbours Left s1

==

not the aql query will give a float 3.2 for s1
and a tag Left (type 'g') for s2

Table maker is this case would have imposed 'float'
and just export a void cell,
aql reports a detailled error message, which is nice,
although a bit cryptic, sorry

1) do you have a suggestion to improve the error message
2) the solu is to select on m[1]==Position
   or on selecting  p from m.Position or maybe m[Position]
   (i am never sure of the aql syntax, but something like this
   works)
   naming tags is more secure than offsets if you access
   constructed types, and more robust if the schema changes in the
   future and gets enriched

Please let me know if the explanation is clear enough

>This comes from the following aql query, explorable at 
>http://grain.jouy.inra.fr/cgi-bin/ace/custom/aqlInterface/graingenes :
>
>select l, m, p
>from s in class sequence where exists_tag s->dna_homol,
>     l in s->probe->locus,
>     m in l->map,
>     p in m[2]
>
>
>I routinely aql out every map position in the database using a different
>query, but it gets them all with no errors, so this is strange.
>
>This is using ace4_9t.
>
>- Dave
>
>-   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -
>David E. Matthews, PhD            USDA-ARS Plant Genome Database Curator
>Cornell University                Email: matthews <at> greengenes.cit.cornell.edu
>Department of Plant Breeding                          Phone: +1-607-255-9951 
>409 Bradfield Hall                                      Fax: +1-607-255-6683
>Ithaca, New York 14853, USA             GrainGenes: http://wheat.pw.usda.gov
>
>_______________________________________________
>Acedb mailing list
>Acedb <at> net.bio.net
>http://www.bio.net/biomail/listinfo/acedb

Dave Matthews | 14 Mar 2007 03:08
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aql error 810, Inconsistent value types

What does this error message mean?

// AQL error 810 around: 'l, m, p from s in'
//                              ^
// Inconsistent value types in table column 3
// Value type was 'g' and now the field evaluates to type 'f' in row 19822

What are value types g and f?

This comes from the following aql query, explorable at 
http://grain.jouy.inra.fr/cgi-bin/ace/custom/aqlInterface/graingenes :

select l, m, p
from s in class sequence where exists_tag s->dna_homol,
     l in s->probe->locus,
     m in l->map,
     p in m[2]

I routinely aql out every map position in the database using a different
query, but it gets them all with no errors, so this is strange.

This is using ace4_9t.

- Dave

-   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -   -
David E. Matthews, PhD            USDA-ARS Plant Genome Database Curator
Cornell University                Email: matthews <at> greengenes.cit.cornell.edu
Department of Plant Breeding                          Phone: +1-607-255-9951 
409 Bradfield Hall                                      Fax: +1-607-255-6683
Ithaca, New York 14853, USA             GrainGenes: http://wheat.pw.usda.gov

Ed Griffiths | 14 Oct 2006 13:46
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Acedb bug....

All,

Following a report by a user at Sanger I have found a serious bug has been 
introduced into the way acedb parses in data, the bug has been in the code for 
several years so its surprising it has not come to light before.

The problem can be summarised as follows, if you parse in the following file:

//------start--------
CDS : "R09E10.1"

Sequence : "Eds_sequence"
CDS_child "R09E10.1" 11111 22222

Sequence : "R09E10"
-D CDS_child "R09E10.1" 11111 22222
CDS_child "R09E10.1" 33333 44444
//------------end-----

You end up with "R09E10" looking like this:

Sequence R09E10
   SMap    S_Child     CDS_child   R09E10.1

i.e. you have lost the new coordinates from your change.

There is a work around in that if you do the deletion and addition in two stages 
then all will be fine:

Sequence : "R09E10"
-D CDS_child "R09E10.1" 11111 22222

Sequence : "R09E10"
CDS_child "R09E10.1" 33333 44444

I am urgently looking to find when this problem was introduced and to fix it.

Ed
--

-- 
  ------------------------------------------------------------------------
| Ed Griffiths, Acedb development, Informatics Group,                    |
|  The Morgan Building, Sanger Institute, Wellcome Trust Genome Campus   |
|  Hinxton, Cambridge CB10 1HH                                           |
|                                                                        |
| email: edgrif <at> sanger.ac.uk  Tel: +44-1223-496844  Fax: +44-1223-494919 |
  ------------------------------------------------------------------------

Prof.Roland Wagner | 16 Sep 2006 11:59
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BIRD: Deadline Extension: Sepptember 22 2006

*CALL FOR PAPERS*

*&*

*CALL FOR POSTERS*

* *

* *

*1st International Conference*

*on*

* *

*Bioinformatics Research and Development*

* B I R D '07***

*http://www.birdconf.org* <http://www.birdconf.org/>**

* *

*Berlin**, Germany***

*March 12-14, 2007*

*Keynote Talk:*

* *

*Josef Penninger*
Institute of Molecular Biotechnology (IMBA)

http://www.imba.oeaw.ac.at/index.php?id=115

*Scope of the conference:*

* *

The primary focus of BIRD '07 is to provide researchers and users in the 
field of bioinformatics a forum in which to interact about new research 
directions, developments, and software/web services.

It encompasses the methods of solving biological, medical, or chemical 
problems by computer science, machine learning, or information 
processing tools.

The conceptual level of the methods range from theoretical approaches 
through the design of algorithms, models, and information processing 
systems through to the development of software packages and web services.

The program committee seeks contributions, which topics include, but are 
not limited to:

* *

    * Algebraic Biology
    * Databases & Data Integration
    * Drug Design
    * Ontologies & Textmining
    * Evolution and Phylogenetics
    * Genomics
    * Gene and Splice Site Recognition
    * Machine Learning and Data Analysis
    * Gene Expression/Regulation & Microarrays
    * MicroRNA and RNAi
    * Molecular Diagnostics and Treatment Support
    * Molecular Dynamics
    * Pathways, Networks, Systems Biology
    * Phylogenetics & Molecular Evolution
    * Protein & RNA Structure and Function
    * Proteomics
    * Sequence Analysis & Alignment
    * SNPs and Haplotyping
    * Systems Biology and Modelling

* *

*General Chair:*

Roland Wagner, FAW, University of Linz, Austria

*Program Chair:*

Sepp Hochreiter, University of Linz, Austria

* *

*Program Committee (Steering):*

Amos Bairoch, Swiss Institute of Bioinformatics, Switzerland

Pierre Baldi, University of California, Irvine, USA

Philip E. Bourne, UCSD, USA

Cornelius Frömmel, Georg-August-Universität Göttingen, Germany

David Gilbert, University of Glasgow, UK

Amarnath Gupta, SDSC of the University of California San Diego, USA

Knut Reinert, FU Berlin, Germany

Hershel Safer, Weizmann Institute of Science, Israel

Erik Sonnhammer, Stockholm University, Sweden

and about 200 other PC-members

* *

*Paper and Poster Submission Details:
*Authors are invited to submit original research contributions or 
experience reports in English.
Paper registration and electronic submission will start in August 2006.

Submitted papers will be carefully evaluated based on originality, 
significance, technical soundness, and clarity of exposition.

*Papers:*
Please submit your paper as PDF file only. Paper submissions in LNCS format
(http://www.springer.de/comp/lncs/authors.html) would be highly 
appreciated.
In order to avoid problems in viewing and printing your paper, please,
only use embedded fonts. Please, do not use language extensions
(e.g., Chinese language support) neither in texts nor in figures.
The submitted manuscript should closely reflect the final paper as it will
appear in the Proceedings.
Papers should not exceed 15 pages in LNCS format.
Any submission that exceeds length limits or deviates from formatting
requirements may be rejected without review.

*Posters:*
Please submit an extended abstract or short paper version of your poster
as PDF file only.

*Important Dates:*

    * Submission of Full Papers: September 22, 2006
    * Noification of Acceptance: November 20, 2006
    * Camera-ready Copies of papers: December 20, 2006

For further inquiries, please contact the BIRD Conference Organisation 
Office (office <at> birdconf.org <mailto:office <at> birdconf.org>)

All accepted conference papers will be published in "Lecture Notes in 
Bioinformatics" (LNBI) by Springer Verlag.

All accepted poster will be published by the Austrian Computer Society.

-- 
Univ. Prof. Dr. Roland Wagner 
Director of the Institute of Applied Knowledgeprocessing  (FAW)
Director of the Institute "integriert studieren" 

Tel.: +43 676 84673210
Fax: +43 732 24689308 
rrwagner <at> faw.uni-linz.ac.at 

sec1: Monika Neubauer 
Tel.: +43 676 84673212 
Fax.:+43 732 2468 9308 
mneubauer <at> faw.uni-linz.ac.at

sec2: Barbara  Arrer
Tel: +43 732 2468 9232
Fax:+43 732 2468 9322
barbara.arrer <at> jku.ta

http://www.faw.uni-linz.ac.at 
http://www.integriert-studieren.jku.at 
http://www.dexa.org 
http://www.icchp.org

Ed Griffiths | 30 Mar 2006 16:06
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acedb 4.9 news.

All,

I tried to post this a couple of days ago but it seems not to have go through.

Time moves on and the GTK graphics toolkit that acedb 4.9.* uses has moved on a 
lot. Currently acedb 4.9 is compiled against GTK version 1.2 and the latest 
stable version of GTK is version 2.6. GTK 1.2 is now not regularly installed 
except as the libraries on our systems and it makes sense to move on.

I am proposing to do the following:

1) Make a special download link for the current development release of acedb 
which will remain parmanently on our website as  acedb/GKT1, the code will be 
available as both statically and dynamically linked versions.

2) From now on make versions of acedb that are linked against GTK version 2.6. 
This is the most stable current version of gtk (see www.gtk.org). I will make 
dynamically linked versions but not statically linked. Making the statically 
linked versions is painful and the binaries produced exceed the filesize limit 
for our external website so that they are only available via ftp.

I intend to start this process at the end of April. Please let me have any 
comments/problems etc before then.

thanks, Ed
  --
  ------------------------------------------------------------------------
| Ed Griffiths, Acedb development, Informatics Group,                    |
|  The Morgan Building, Sanger Institute, Wellcome Trust Genome Campus   |
|  Hinxton, Cambridge CB10 1HH                                           |
|                                                                        |
| email: edgrif <at> sanger.ac.uk  Tel: +44-1223-496844  Fax: +44-1223-494919 |
  ------------------------------------------------------------------------

Nicolas Thierry-Mieg | 23 Feb 2006 16:31
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Protein subclass

hi all,

I am trying to define a subclass named Protein, but this doesn't work 
with any tested xace versions (current supported or daily)
Is this forbidden? If yes, shouldn't xace/tace complain when it reads 
the models?

Here is a small example to illustrate:

######################################
$ more models.wrm
?Ligand Protein
         Sugar

######################################
$ more subclasses.wrm
Class Prot
Visible
Is_a_subclass_of Ligand
Filter Protein

Class Protein
Visible
Is_a_subclass_of Ligand
Filter Protein

Class Sugar
Visible
Is_a_subclass_of Ligand
Filter Sugar

######################################
$ more test.ace
Ligand : "lig1"
Protein

Ligand : "lig2"
Sugar

######################################

Initializing the database works fine
When parsing test.ace, no errors

object lig2 is OK, and shows up in class Sugar
but lig1 is NOT in class Protein (ace says that class Protein is empty), 
although it does show up fine in class Prot.

thanks
nicolas

--

-- 
------------------------------------------------------------
Nicolas Thierry-Mieg
Laboratoire LSR-IMAG, BP 53, 38041 Grenoble Cedex 9, France
tel : (33/0)4-76-63-55-79, fax : (33/0)4-76-63-55-50
------------------------------------------------------------

Jing Yu | 14 Feb 2006 20:28
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Re: What AceDB "Error status = 139" means?

Nicolas,

No error appears after setting up ulimit -s unlimited, and
everything looks fine.  Thank you very much!!

Jing

On Tue, 14 Feb 2006, Nicolas Thierry-Mieg wrote:

>
> bash is fine
>
> ...
> ulimit -a
> to see your current limits
> 
> then eg to set the stack size to max, type:
> ulimit -s unlimited 
>                
> 
> this will only change the limits for your current shell, hence you
> should call tace from it
> 
> when satisfied you can put the correct ulimit commands in your
> .bash_profile to make the changes affect every new shell
>                
>                
> try setting every value to unlimited, at least the memory related ones
> (except core, which you can set to 0 since you probably don't read core
> dumps anyways)


Gmane