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From: Bruz M. <bma...@sy...> - 2010-10-04 17:51:46
|
Hi Doan, I was forwarded your question on SBEAMS support of Affymetrix data generated by AGCC as opposed to GCOS. We originally handled Affy data upload by taking the XML files that GCOS provided and populating the database from these. AGCC doesn't produce these XML files so our existing uploader didn't work on them, however since we'd originally built our GCOS support we created a separate LIMS system for our microarray facility called SLIMarray (http://slimarray.systemsbiology.net). We now use a data loading script that polls SLIMarray for new array data and then loads them into SBEAMS, so you would either have the option of using SLIMarray in conjunction with SBEAMS or updating the old XML data loader to work with the newer ARR files that AGCC produces. In terms of BioConductor, it has supported the new CEL file format that AGCC produces for the last couple of years, so any recent version should be able to handle your AGCC data. Thanks, Bruz > ---------- Forwarded message ---------- > From: Nguyen, Doan <DN...@ls...> > Date: Thu, Sep 30, 2010 at 2:21 PM > Subject: [SBEAMS-discuss] sbeams install > To: sbe...@li... > > > I have AGCC installed on windows server 2003, MS SQL 2005. I want to install > sbeams on the same server and build pipeline to input data generated from > AGCC directly to sbeams for further analysis. Is there any issue with > that-GCOS vs AGCC compatibility for generating this pipeline? > > > > --------------------------------- > > Doan H. Nguyen, PhD > > Genetics and Gene Therapy Program > > Director, Microarray Core and Genome Bioinformatics Center > > 533 Bolivar St., Rm 539 CSRB > > New Orleans, LA 70112 > > Tel: (504) 568-4552 > > Lab: (504) 568-8001 > > Fax: (504) 568-8500 > > Email: dn...@ls... > > ------------------------------------------ > > > > ------------------------------------------------------------------------------ > Start uncovering the many advantages of virtual appliances > and start using them to simplify application deployment and > accelerate your shift to cloud computing. > http://p.sf.net/sfu/novell-sfdev2dev > _______________________________________________ > Sbeams-discuss mailing list > Sbe...@li... > https://lists.sourceforge.net/lists/listinfo/sbeams-discuss > > > |
|
From: Nguyen, D. <DN...@ls...> - 2010-09-30 21:21:49
|
I have AGCC installed on windows server 2003, MS SQL 2005. I want to install sbeams on the same server and build pipeline to input data generated from AGCC directly to sbeams for further analysis. Is there any issue with that-GCOS vs AGCC compatibility for generating this pipeline? --------------------------------- Doan H. Nguyen, PhD Genetics and Gene Therapy Program Director, Microarray Core and Genome Bioinformatics Center 533 Bolivar St., Rm 539 CSRB New Orleans, LA 70112 Tel: (504) 568-4552 Lab: (504) 568-8001 Fax: (504) 568-8500 Email: dn...@ls... ------------------------------------------ |
|
From: Philippe G. <phi...@uh...> - 2010-09-27 10:37:40
|
Hello, I am trying to load in the proteomics module the files that come out of Sequest (.dta, .out). According to what I have seen in the source code of the script load_proteomics_experiment.pl, they must be in a subdirectory whose name is the same as the tag of the fraction. But how is it possible to create fractions? Thank you! Best regards, Philippe |
|
From: Philippe G. <phi...@uh...> - 2010-09-21 15:16:57
|
Hello, I am trying to install the proteomics module for Sbeams. Section 8 of the installation notes say that we should find the script load_biosequence_st.pl in the directory $BEAMS/lib/scrips/Proteomics. But it is not there. There are other scripts like load_proteomics_experiment.pl for example but not the one for which I write. I have searched but I find it nowhere. Where could I find it? If it is not there, I assume it will be a problem for the rest of the installation (?). Thank you for your help. Cheers, Philippe |
|
From: Bonjour, F. <Fil...@pm...> - 2009-07-28 07:42:02
|
Dear SBEAMS community, Thank you for all your help installing and configuring SBEAMS so far. Having downloaded the sample data from http://www.sbeams.org/sample_data/, we are experiencing some difficulty uploading it (in this case Affymetrix .CEL files) into the SBEAMS database. Alternatively, it seems that SBEAMS can be directly connected to a central data repository. Question 1: How can we set the central repository within SBEAMS Microarray? Question 2: How is it possible to read .CEL files from a local folder? Question 3: If it's not possible to read .CEL files directly into SBEAMS, then I assume that the files are downloadable from the site above so we can setup a repository ourselves. Are there instructions to do this? Thanks in advance for your help! Filipe |
|
From: Dave C. <dca...@sy...> - 2009-07-09 14:55:28
|
Filipe,
Not really, the documentation should be accurate and complete -
including the default params file. I'll update that, thanks for your
patience.
-Dave
On Thu, Jul 9, 2009 at 3:08 AM, Bonjour,
Filipe<Fil...@pm...> wrote:
> Dear Dave,
>
> Thanks, I completely zapped the SMB config lines. For the logs, LOG_BASE_DIR is not in SBEAMS.conf, though it's mentioned in a comment:
>
> # Directory to which affy log files will be written, if not set will default
> # to LOG_BASE_DIR above, else $sbeams/var/log.
> CONFIG_SETTING{MA_LOG_BASE_DIR} = var/logs
>
> My bad, I should have aguessed both.
>
> Filipe
>
> ---
>
> Filipe Bonjour
> Philip Morris International IT Service Center Sàrl
> R&D High Performance Computing
> E-mail: Fil...@pm...
> Phone: +41 58 242 7772
> Fax: +41 58 242 0101
> Web: http://itsc-businesspoint.app.pmi
>
> -----Original Message-----
> From: Dave Campbell [mailto:dca...@sy...]
> Sent: 08 July 2009 19:36
> To: General questions and discussion about SBEAMS
> Subject: Re: [SBEAMS-discuss] General questions
>
> Filipe,
>
> I've made some initial answers to some of your questions below.
>
>
>> I am a beginner with SBEAMS, and I was asked to install it (SVN 6206, 6th July 2009), as well as the modules:
>>
>> * Proteomics
>> * Microarray
>> * SNP
>> * Biomarker
>
>> Security
>> --------
>>
>> We installed a software to use Windows Active Directory users in Linux, so the users do not exist in /etc/passwd or in NIS. I can easily get around this when installing modules by creating a temporary user. However, it seems that for some modules human users have to run some commands (e.g. "./load_biosequence_set.pl" in proteomics). Is there any way to avoid the check against /etc/passwd?
>
> You can also authenticate vs. Windows domain controller, by enabling this in SBEAMS.conf and setting values for the primary and backup domain controllers.
>
> SMBAUTH{ENABLE} = YES
> SMBAUTH{PDC} = XXX
> SMBAUTH{BDC} = XXX
> SMBAUTH{Domain} = XXX
>
> If this doesn't work, we might be able to implement authentication vs.
> a Windows Active directory server, if there is a perl module for this.
> Or you could implement and we could enter the code in SVN!
>
>
>> Logging
>> -------
>>
>> How can I enable logging system-wide? My log files in $SBEAMS/var/logs (debug.log, error.log, etc.) all contains only a single line "Initializing". I couldn't find a setting in SBEAMS.conf, not some variable in Log.pm.
>
> Make sure the files are writable, pointed to by the LOG_BASE_DIR, then try setting the logging level to debug. Once this is done, click around and you should get some output in these files.
>
> LOGGING_LEVEL = debug
> LOG_BASE_DIR = /net/dblocal/www/html/dev2/sbeams/var/logs
>
> -Dave
>
> ------------------------------------------------------------------------------
> Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge _______________________________________________
> Sbeams-discuss mailing list
> Sbe...@li...
> https://lists.sourceforge.net/lists/listinfo/sbeams-discuss
>
>
>
> ------------------------------------------------------------------------------
> Enter the BlackBerry Developer Challenge
> This is your chance to win up to $100,000 in prizes! For a limited time,
> vendors submitting new applications to BlackBerry App World(TM) will have
> the opportunity to enter the BlackBerry Developer Challenge. See full prize
> details at: http://p.sf.net/sfu/Challenge
> _______________________________________________
> Sbeams-discuss mailing list
> Sbe...@li...
> https://lists.sourceforge.net/lists/listinfo/sbeams-discuss
>
|
|
From: Bonjour, F. <Fil...@pm...> - 2009-07-09 11:29:00
|
Dear Dave, Yes, we're using MS-SQL 2005. Here is what I guess is another small bug -- this time in the module SNP. The CREATETABLES file generated automatically has the following definition for the table selected_snp: CREATE TABLE sbeams.dbo.selected_snp ( selected_snp_id varchar IDENTITY(255) NOT NULL, snp_selection_run_id int NOT NULL, jared_id varchar(255) NOT NULL, <... etc ...> ) IDENTITY is not compatible with character-type columns. By the way, this column selected_snp_id has a FOREIGN KEY constraint to a table called SN_snp which does not exist. Thanks again! Filipe --- Filipe Bonjour Philip Morris International IT Service Center Sàrl R&D High Performance Computing E-mail: Fil...@pm... Phone: +41 58 242 7772 Fax: +41 58 242 0101 Web: http://itsc-businesspoint.app.pmi -----Original Message----- From: Dave Campbell [mailto:dca...@sy...] Sent: 08 July 2009 19:44 To: General questions and discussion about SBEAMS Subject: Re: [SBEAMS-discuss] Proteomics questions Filipe, Again, I've made a first-pass at answering your questions. > Proteomics > ========== > > Separate databases? > ------------------- > > To minimize install problems, I planned to put some modules (here, Proteomics) in a separate database. The CREATETABLES script worked perfectly, but the POPULATE script then tried to populate some tables (e.g. work_group) in the separate database instead of Core. I have given up trying to install modules in separate darabases for now because I'm under a little pressure to get SBEAMS working, but I would like to try it again in a separate site that I can play with. Any advice on this would be appreciated. Our intent was to make all modules installable into the same database, or into separate databases, as the user desired. In practice, some differences in table structure exist and some of the setup scripts, as you found out, may assume an empty db. At our site each of the modules has its own physical SQL server database. Are you using mysql or SQL Server? > > Bug report > ---------- OK, I fixed that and checked it in. I assume this answers my previous question, because the error was in the mssql version of the POPULATE script. Thanks for the bug report. If you have more, maybe we'll set you up with our bug database. -Dave > > There is a small bug in the Proteomics module. Line 204 in the POPULATE file is missing an end quote: > > Proteomics_POPULATE.mssql:204:VALUES ( > 'CBS_display_options','DifferentSequence','Show different-sequence > matches,50 ); > > I apologize if this is not the proper channel to submit bugs. > > Thanks in advance! > > Filipe > > > > ---------------------------------------------------------------------- > -------- Enter the BlackBerry Developer Challenge This is your chance > to win up to $100,000 in prizes! For a limited time, vendors > submitting new applications to BlackBerry App World(TM) will have the > opportunity to enter the BlackBerry Developer Challenge. See full > prize details at: http://p.sf.net/sfu/Challenge > _______________________________________________ > Sbeams-discuss mailing list > Sbe...@li... > https://lists.sourceforge.net/lists/listinfo/sbeams-discuss > ------------------------------------------------------------------------------ Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge _______________________________________________ Sbeams-discuss mailing list Sbe...@li... https://lists.sourceforge.net/lists/listinfo/sbeams-discuss |
|
From: Bonjour, F. <Fil...@pm...> - 2009-07-09 10:09:20
|
Dear Dave,
Thanks, I completely zapped the SMB config lines. For the logs, LOG_BASE_DIR is not in SBEAMS.conf, though it's mentioned in a comment:
# Directory to which affy log files will be written, if not set will default
# to LOG_BASE_DIR above, else $sbeams/var/log.
CONFIG_SETTING{MA_LOG_BASE_DIR} = var/logs
My bad, I should have aguessed both.
Filipe
---
Filipe Bonjour
Philip Morris International IT Service Center Sàrl
R&D High Performance Computing
E-mail: Fil...@pm...
Phone: +41 58 242 7772
Fax: +41 58 242 0101
Web: http://itsc-businesspoint.app.pmi
-----Original Message-----
From: Dave Campbell [mailto:dca...@sy...]
Sent: 08 July 2009 19:36
To: General questions and discussion about SBEAMS
Subject: Re: [SBEAMS-discuss] General questions
Filipe,
I've made some initial answers to some of your questions below.
> I am a beginner with SBEAMS, and I was asked to install it (SVN 6206, 6th July 2009), as well as the modules:
>
> * Proteomics
> * Microarray
> * SNP
> * Biomarker
> Security
> --------
>
> We installed a software to use Windows Active Directory users in Linux, so the users do not exist in /etc/passwd or in NIS. I can easily get around this when installing modules by creating a temporary user. However, it seems that for some modules human users have to run some commands (e.g. "./load_biosequence_set.pl" in proteomics). Is there any way to avoid the check against /etc/passwd?
You can also authenticate vs. Windows domain controller, by enabling this in SBEAMS.conf and setting values for the primary and backup domain controllers.
SMBAUTH{ENABLE} = YES
SMBAUTH{PDC} = XXX
SMBAUTH{BDC} = XXX
SMBAUTH{Domain} = XXX
If this doesn't work, we might be able to implement authentication vs.
a Windows Active directory server, if there is a perl module for this.
Or you could implement and we could enter the code in SVN!
> Logging
> -------
>
> How can I enable logging system-wide? My log files in $SBEAMS/var/logs (debug.log, error.log, etc.) all contains only a single line "Initializing". I couldn't find a setting in SBEAMS.conf, not some variable in Log.pm.
Make sure the files are writable, pointed to by the LOG_BASE_DIR, then try setting the logging level to debug. Once this is done, click around and you should get some output in these files.
LOGGING_LEVEL = debug
LOG_BASE_DIR = /net/dblocal/www/html/dev2/sbeams/var/logs
-Dave
------------------------------------------------------------------------------
Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge _______________________________________________
Sbeams-discuss mailing list
Sbe...@li...
https://lists.sourceforge.net/lists/listinfo/sbeams-discuss
|
|
From: Dave C. <dca...@sy...> - 2009-07-08 17:46:07
|
Filipe, This module was developed with hopes of having it adopted by our proteomics lab as a sort of sample LIMS. The lab in question lost interest rather quickly, so development of this module stopped in a rather incomplete state. -Dave > > I am a beginner with SBEAMS, and I was asked to install it (SVN 6206, 6th July 2009), as well as the modules: > > * Proteomics > * Microarray > * SNP > * Biomarker > > The installation of Core, Tools and BioLink was a little long (you have to get used to the system) but completed without significant issues. The modules caused me more trouble. I would appreciate comments on my remarks below, and help with my problems. I will split my questions in separate emails. > > Biomarker > ========= > > Biomarker was a cause of trouble for me... perhaps because the documentation is very incomplete (only the dependences section is there). The main problem is that the CREATECONSTRAINTS file refers to an external table called AT_tissue_type which I could not find anywhere. > > Thanks in advance! > > Filipe > > ------------------------------------------------------------------------------ > Enter the BlackBerry Developer Challenge > This is your chance to win up to $100,000 in prizes! For a limited time, > vendors submitting new applications to BlackBerry App World(TM) will have > the opportunity to enter the BlackBerry Developer Challenge. See full prize > details at: http://p.sf.net/sfu/Challenge > _______________________________________________ > Sbeams-discuss mailing list > Sbe...@li... > https://lists.sourceforge.net/lists/listinfo/sbeams-discuss > |
|
From: Dave C. <dca...@sy...> - 2009-07-08 17:44:12
|
Filipe, Again, I've made a first-pass at answering your questions. > Proteomics > ========== > > Separate databases? > ------------------- > > To minimize install problems, I planned to put some modules (here, Proteomics) in a separate database. The CREATETABLES script worked perfectly, but the POPULATE script then tried to populate some tables (e.g. work_group) in the separate database instead of Core. I have given up trying to install modules in separate darabases for now because I'm under a little pressure to get SBEAMS working, but I would like to try it again in a separate site that I can play with. Any advice on this would be appreciated. Our intent was to make all modules installable into the same database, or into separate databases, as the user desired. In practice, some differences in table structure exist and some of the setup scripts, as you found out, may assume an empty db. At our site each of the modules has its own physical SQL server database. Are you using mysql or SQL Server? > > Bug report > ---------- OK, I fixed that and checked it in. I assume this answers my previous question, because the error was in the mssql version of the POPULATE script. Thanks for the bug report. If you have more, maybe we'll set you up with our bug database. -Dave > > There is a small bug in the Proteomics module. Line 204 in the POPULATE file is missing an end quote: > > Proteomics_POPULATE.mssql:204:VALUES ( 'CBS_display_options','DifferentSequence','Show different-sequence matches,50 ); > > I apologize if this is not the proper channel to submit bugs. > > Thanks in advance! > > Filipe > > > > ------------------------------------------------------------------------------ > Enter the BlackBerry Developer Challenge > This is your chance to win up to $100,000 in prizes! For a limited time, > vendors submitting new applications to BlackBerry App World(TM) will have > the opportunity to enter the BlackBerry Developer Challenge. See full prize > details at: http://p.sf.net/sfu/Challenge > _______________________________________________ > Sbeams-discuss mailing list > Sbe...@li... > https://lists.sourceforge.net/lists/listinfo/sbeams-discuss > |
|
From: Dave C. <dca...@sy...> - 2009-07-08 17:36:44
|
Filipe,
I've made some initial answers to some of your questions below.
> I am a beginner with SBEAMS, and I was asked to install it (SVN 6206, 6th July 2009), as well as the modules:
>
> * Proteomics
> * Microarray
> * SNP
> * Biomarker
> Security
> --------
>
> We installed a software to use Windows Active Directory users in Linux, so the users do not exist in /etc/passwd or in NIS. I can easily get around this when installing modules by creating a temporary user. However, it seems that for some modules human users have to run some commands (e.g. "./load_biosequence_set.pl" in proteomics). Is there any way to avoid the check against /etc/passwd?
You can also authenticate vs. Windows domain controller, by enabling
this in SBEAMS.conf and setting values for the primary and backup
domain controllers.
SMBAUTH{ENABLE} = YES
SMBAUTH{PDC} = XXX
SMBAUTH{BDC} = XXX
SMBAUTH{Domain} = XXX
If this doesn't work, we might be able to implement authentication vs.
a Windows Active directory server, if there is a perl module for this.
Or you could implement and we could enter the code in SVN!
> Logging
> -------
>
> How can I enable logging system-wide? My log files in $SBEAMS/var/logs (debug.log, error.log, etc.) all contains only a single line "Initializing". I couldn't find a setting in SBEAMS.conf, not some variable in Log.pm.
Make sure the files are writable, pointed to by the LOG_BASE_DIR, then
try setting the logging level to debug. Once this is done, click
around and you should get some output in these files.
LOGGING_LEVEL = debug
LOG_BASE_DIR = /net/dblocal/www/html/dev2/sbeams/var/logs
-Dave
|
|
From: Bonjour, F. <Fil...@pm...> - 2009-07-08 17:22:29
|
Dear SBEAMS Community, I am a beginner with SBEAMS, and I was asked to install it (SVN 6206, 6th July 2009), as well as the modules: * Proteomics * Microarray * SNP * Biomarker The installation of Core, Tools and BioLink was a little long (you have to get used to the system) but completed without significant issues. The modules caused me more trouble. I would appreciate comments on my remarks below, and help with my problems. I will split my questions in separate emails. SNP === I had several difficulties with SNP, perhaps because there are no install instructions. The first problem is that there is a static script SNP_Create_Tables.sql and at the same time there is a dynamically generated one, SNP_CREATETABLES.mssql. I ran the dynamic one followed by the static one, despite the fact that they create some tables in common with different table definitions. Then, I had problems with the constraints. Ignoring any errors due to the fact that some constraints already existed, this one persists: "DBD::Sybase::db do failed: Server message number=1767 severity=16 state=0 line=1 server=PMICHLAUHPC01\RDSQLHPC01 text=Foreign key 'fk_selected_snp_selected_snp_id' references invalid table 'sbeamsdev.dbo.SN_snp'." The table SN_snp is not in any of the CREATETABLE file. Did I miss a module dependency? Thanks in advance! Filipe |
|
From: Bonjour, F. <Fil...@pm...> - 2009-07-08 17:21:37
|
Dear SBEAMS Community, I am a beginner with SBEAMS, and I was asked to install it (SVN 6206, 6th July 2009), as well as the modules: * Proteomics * Microarray * SNP * Biomarker The installation of Core, Tools and BioLink was a little long (you have to get used to the system) but completed without significant issues. The modules caused me more trouble. I would appreciate comments on my remarks below, and help with my problems. I will split my questions in separate emails. Biomarker ========= Biomarker was a cause of trouble for me... perhaps because the documentation is very incomplete (only the dependences section is there). The main problem is that the CREATECONSTRAINTS file refers to an external table called AT_tissue_type which I could not find anywhere. Thanks in advance! Filipe |
|
From: Bonjour, F. <Fil...@pm...> - 2009-07-08 17:20:50
|
Dear SBEAMS Community, I am a beginner with SBEAMS, and I was asked to install it (SVN 6206, 6th July 2009), as well as the modules: * Proteomics * Microarray * SNP * Biomarker The installation of Core, Tools and BioLink was a little long (you have to get used to the system) but completed without significant issues. The modules caused me more trouble. I would appreciate comments on my remarks below, and help with my problems. I will split my questions in separate emails. Proteomics ========== Separate databases? ------------------- To minimize install problems, I planned to put some modules (here, Proteomics) in a separate database. The CREATETABLES script worked perfectly, but the POPULATE script then tried to populate some tables (e.g. work_group) in the separate database instead of Core. I have given up trying to install modules in separate darabases for now because I'm under a little pressure to get SBEAMS working, but I would like to try it again in a separate site that I can play with. Any advice on this would be appreciated. Bug report ---------- There is a small bug in the Proteomics module. Line 204 in the POPULATE file is missing an end quote: Proteomics_POPULATE.mssql:204:VALUES ( 'CBS_display_options','DifferentSequence','Show different-sequence matches,50 ); I apologize if this is not the proper channel to submit bugs. Thanks in advance! Filipe |
|
From: Bonjour, F. <Fil...@pm...> - 2009-07-08 17:20:13
|
Dear SBEAMS Community, I am a beginner with SBEAMS, and I was asked to install it (SVN 6206, 6th July 2009), as well as the modules: * Proteomics * Microarray * SNP * Biomarker The installation of Core, Tools and BioLink was a little long (you have to get used to the system) but completed without significant issues. The modules caused me more trouble. I would appreciate comments on my remarks below, and help with my problems. I will split my questions in separate emails. General questions ================= Security -------- We installed a software to use Windows Active Directory users in Linux, so the users do not exist in /etc/passwd or in NIS. I can easily get around this when installing modules by creating a temporary user. However, it seems that for some modules human users have to run some commands (e.g. "./load_biosequence_set.pl" in proteomics). Is there any way to avoid the check against /etc/passwd? Logging ------- How can I enable logging system-wide? My log files in $SBEAMS/var/logs (debug.log, error.log, etc.) all contains only a single line "Initializing". I couldn't find a setting in SBEAMS.conf, not some variable in Log.pm. Thanks in advance! Filipe |
|
From: Dave C. <dca...@sy...> - 2007-07-05 06:40:46
|
Hi; BioLink stores biological information from external sources and = provides this to any other module(s). Along with 'Core' it is one of = the 2 prerequisite modules for any SBEAMS installation. The main = BioLink script, used to load GO annotations, is documented in the = install notes.=20 The load_kegg_pathways scripts uses SOAP calls to KEGG to populate = tables of pathways and genes that belong to them. These are used = primarily by the PeptideAtlas and Glycopeptde modules, although they = could someday be useful other modules as well. Some of the scripts will = honor the 'h or --help flag, and most can be tricked into printing a = usage statement by using a nonsensical argument, such as --zqty >./load_kegg_pathways.pl -zqty [Wed Jul 4 23:39:54 2007] load_kegg_pathways.pl: Unknown option: zqty Must specify one and only one of i/u/d Usage: load_kegg_pathways.pl mode(-u or -d or -i) [-o organism] -i --insert Insert only missing data, do not overwrite existing = records -u --update Update pathway/gene info for selected organism or all -i --delete Delete genes/pathway info from db -o --organism Complete actions for specified organism(s); defaults to = all If you have any questions about specific scripts, please let us know. -Dave I'm a french student in bioinformatics master degree at university of =20 Rouen and I installed SBEAMS in the lab where i'm trainee. Sbeams, Biolink and MicroArray module are working, but i don't =20 understand very well what's mains goals about Biolink module ? Could you please explain me how do to use this module ? And how use =20 differents scripts like load_kegg_pathways.pl ... Thank you very much. Germain Paimparay -------------------------------------------------------------------------= This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Sbeams-discuss mailing list Sbe...@li... https://lists.sourceforge.net/lists/listinfo/sbeams-discuss |
|
From: Germain P. <ger...@et...> - 2007-07-04 07:12:10
|
Hello SBEAMS Team. I'm a french student in bioinformatics master degree at university of Rouen and I installed SBEAMS in the lab where i'm trainee. Sbeams, Biolink and MicroArray module are working, but i don't understand very well what's mains goals about Biolink module ? Could you please explain me how do to use this module ? And how use differents scripts like load_kegg_pathways.pl ... Thank you very much. Germain Paimparay |
|
From: Dave C. <dca...@sy...> - 2007-06-05 17:13:50
|
Germain;
Approximately how many arrays are you processing as a batch? We have
seen memory problems at the normalization stage, and there is a way to
mitigate this. On the last page you fill out prior to starting the
normalization, you can deselect the options that say "Produce MVA
scatter plot among members of each sample group" and "Produce
correlation matrix for this normalization set". When either of these
are selected, a more memory intensive R method is used to read the CEL
files [ readAffy() ].
If you were able to normalize a group of files and then ran out of
memory while running SAM or t test, we'd be interested in seeing the
output/error files. If you look in the directory specified by the
config parameter CONFIG_SETTING{MA_BIOC_DELIVERY_PATH}, there will be
directories for each analysis - the files will be called xxxxx.out and
xxxxx.err, where xxxxx is the directory name.
Please note that the R methods do take a certain amount of memory to
run, and there will be some practical limit (in terms of the number of
arrays which can be processed) based on your computer hardware.
-Dave
>Hello SBEAMS team,
>
>I installed SBEAMS tool (core, and microarray module).
>But when I run one t test or SAM or ratio, R processus use all RAM
>memory (1Go) en crash.
>
>What kind of configuration I needed to run SBEAMS correctly ?
>
>Thank you.
>
>Germain Paimparay
>
>
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From: Germain P. <ger...@et...> - 2007-06-05 16:36:53
|
Hello SBEAMS team, I installed SBEAMS tool (core, and microarray module). But when I run one t test or SAM or ratio, R processus use all RAM memory (1Go) en crash. What kind of configuration I needed to run SBEAMS correctly ? Thank you. Germain Paimparay |
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From: Dave C. <dca...@sy...> - 2007-04-10 16:05:03
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Germain; There are instructions on loading data as well as links to sample data in the Microarray module installation notes. The installation notes can be found in the SBEAMS source tree at $sbeams/doc/Microarray/Microarray_Affy.installnotes, where $sbeams is the root of the source tree. This link is to an online version of the notes: http://www.sbeams.org/devDC/sbeams/doc/Microarray/Microarray_Affy.installnotes SBEAMS is a modular system, and in order to install the Microarray module you will first have to follow the installation instructions for the Core and BioLink modules. If possible, we would suggest using the subversion checkout method to install the system, as this makes getting updates much easier: http://www.sbeams.org/svn.php Please let us know if you have any further questions. -Dave > >I'm french postgraduated student at university of Rouen (France) and >I'm testing SBEAMS online to have an overview of these possibilities >before perhaps install it in local in my lab. > >Your tool is intersting but i don't understand very well how populate >database with affymetrix data (.cel, .csv ...). > >I downloaded tarball realease and saw load scripts, but are there >exist documentation or input files exemples for these scripts ? > > > |
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From: Germain P. <ger...@et...> - 2007-04-10 09:07:23
|
Hello all, I'm french postgraduated student at university of Rouen (France) and I'm testing SBEAMS online to have an overview of these possibilities before perhaps install it in local in my lab. Your tool is intersting but i don't understand very well how populate database with affymetrix data (.cel, .csv ...). I downloaded tarball realease and saw load scripts, but are there exist documentation or input files exemples for these scripts ? Thank you. Geramin Paimparay |
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From: Steve P. <ws...@em...> - 2007-01-04 22:55:08
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> > Hello I'm attempting to install SBEAMS onto a Linux server. This > represents a new install (that is there is no existing SBEAMS > installation on the server). The platform is > as follows: > > CentOS 4.4 2.6.9-42.0.3.ELsmp > mysql 5.0.27 standard > Apache 2 > > I'm using /local/www/html/sbeams (as in the documentation) as the base > locale for SBEAMS. I did this to simplify the installation since this > is what the documentation has. > > Step 1: Installed prereqs. no problems > Step 3:Made edits to Apache conf file indicated in step 3 and > restarted > no problems. > Step 4: Executed as unix user sbeams. no problems. > Step 5: As Mysql user sbeams, I created a database called sbeams > Step 6: No problems > Step 7: Edited SBEAMS.conf > Step 8: Generated the MySQL tables and schema for Module Core > > So now I'm directed to the installation instructions for BioLink but > Step #4 yields a problem for me: > > [sbeams@saf BioLink]$ $SBEAMS/lib/scripts/Core/runsql.pl -s > BioLink_CREATECONSTRAINTS.$DBTYPE -u sbeamsadmin --delimiter semicolon > Enter password, followed by [Enter] (cntl-C to quit): > DBD::mysql::db do failed: Can't create table > './sbeams/#sql-1086_122.frm' > (errno: 150) at /local/www/html/sbeams/lib/scripts/Core/runsql.pl line > 130, > <FIL> line 66. > DBD::mysql::db do failed: Can't create table > './sbeams/#sql-1086_122.frm' > (errno: 150) at /local/www/html/sbeams/lib/scripts/Core/runsql.pl line > 130, > <FIL> line 66. > > ---------------------------- > > I have the impression that I should not be seeing this type of message > at all. However, since it only referenced a a couple of tables I went > ahead and tried to execute step 5 > > ------------------- > [sbeams@saf BioLink]$ ../../scripts/Core/update_driver_tables.pl > BioLink_table_property.txt > Rejected attempt to decrypt non-hex value > Rejected attempt to decrypt non-hex value > [Thu Jan 4 19:19:39 2007] update_driver_tables.pl: WARNING: Unable to > connect to database, please contact SBEAMS Administrator > <sbe...@localdomain.org>: > [Thu Jan 4 19:19:39 2007] update_driver_tables.pl: Access denied for > user > 'sbeams'@'localhost' (using password: YES > ------------------ > > This is most odd since in fact there are in fact valid perms for user > sbeams @ localhost > to connect to the database - I verified this by using: > > mysql -u sbeams -h localhost -p and this worked fine. no problems. > > The only thing that concerns me is that the update_driver_tables.pl > script issues two messages like: > > Rejected attempt to decrypt non-hex value > Rejected attempt to decrypt non-hex value > > which is odd because I used the > $SBEAMS/lib/scripts/Core/encryptDbPasswd.pl -p DB_PASSWORD -c > SBEAMS.conf to populate the database password in SBEAMS.conf. Lets put > it this way. It didn't complain when I executed the earlier steps in > this procedure. According to the installation instructions for BioLink > , if these steps fail then one is supposed to debug. Could you please > advise as to what might be the problem ? Regards, Steve > > ---------------- Steve Pittard BimCore - (BioMolecular Computing Resource at Emory) School of Medicine www.bimcore.emory.edu |
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From: <js...@ad...> - 2006-11-02 19:59:31
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Dave, We are seriously considering and attempt to modify SBEAMS for use with NimbleGen data. I do have one additional question. What is the time frame for adding MAGE-ML support? Thanks, Jeremy ---- Dave Campbell <dca...@sy...> wrote: > > Jeremy; > > The Microarray module currently handles only 2 basic chip types, an in-house spotted array format developed at ISB, and the AffyMetrix platform (see this post for some more detail: http://sourceforge.net/mailarchive/forum.php?thread_id=30282157&forum_id=49971). > > I'm not really familiar with NimbleGen data format, but I suspect it would take a non-trivial amount of work to have make SBEAMS be able to store/analyze it. If you are interested in investigating the feasibility, we would be able to offer some help/suggestions, but have no plans to pursue this. > > Thanks, > > -Dave > > Does anyone have experience using SBEAMS with NimbleGen data? Are there any known issues or obvious problems using SBEAMS with NimbleGen data? > > Thanks, > Jeremy > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Sbeams-discuss mailing list > Sbe...@li... > https://lists.sourceforge.net/lists/listinfo/sbeams-discuss > > > |
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From: Dave C. <dca...@sy...> - 2006-10-26 05:41:09
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Jeremy; The Microarray module currently handles only 2 basic chip types, an = in-house spotted array format developed at ISB, and the AffyMetrix = platform (see this post for some more detail: = http://sourceforge.net/mailarchive/forum.php?thread_id=3D30282157&forum_i= d=3D49971). I'm not really familiar with NimbleGen data format, but I suspect it = would take a non-trivial amount of work to have make SBEAMS be able to = store/analyze it. If you are interested in investigating the = feasibility, we would be able to offer some help/suggestions, but have = no plans to pursue this. Thanks, -Dave Does anyone have experience using SBEAMS with NimbleGen data? Are there = any known issues or obvious problems using SBEAMS with NimbleGen data? Thanks, Jeremy -------------------------------------------------------------------------= Using Tomcat but need to do more? Need to support web services, = security? Get stuff done quickly with pre-integrated technology to make your job = easier Download IBM WebSphere Application Server v.1.0.1 based on Apache = Geronimo http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D= 121642 _______________________________________________ Sbeams-discuss mailing list Sbe...@li... https://lists.sourceforge.net/lists/listinfo/sbeams-discuss |
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From: <js...@ad...> - 2006-10-25 18:01:39
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Does anyone have experience using SBEAMS with NimbleGen data? Are there any known issues or obvious problems using SBEAMS with NimbleGen data? Thanks, Jeremy |