genex-dev — GeneX developers

Re: [GeneX-dev] Embperl vs. Mason: Conclusions

[<ja...@op...>]

"Michael Pear" <mic...@ho...> writes:

> In Embperl, there is a way to set the expiration time for the 
> session cookie. I used 1 day in the Embperl session handling.
> I presume there is something in Apache::Session
> as well. I would say that it is a time period longer than the
> session expiration.

There is also a nice way to expire cookies with CGI.pm, too, but I'm
not sure how to do it with straight mod_perl. Mostly I wanted to know
what time frames sessions should last. Have you gotten any feedback
yet about that? 

One day seems a bit short to me, but I suppose that in the future we
could enable users to configure the timeout and store those values in
the DB, along with other user-specific preferences. 

One thought I just had about cleaning up sessions is what we want is
to only store on session per user. So if we have a us_fk column in the
session table, the INSERT trigger can automatically delete any
sessions with the same user ID. We can still use timestamps, but they
aren't as necessary.

> I think it best to have sessions that persist the browser session
> itself.  

Sorry, I didn't parse this very well. Try again?

> It is nice to come back to working on something without having to
> supply a login.

Agreed. Especially if we start storing more things in the session than
just login info.

jas.

Re: [GeneX-dev] Embperl vs. Mason: Conclusions

[Michael P. <mic...@ho...>]

In Embperl, there is a way to set the expiration time for the 
session cookie. I used 1 day in the Embperl session handling.
I presume there is something in Apache::Session
as well. I would say that it is a time period longer than the
session expiration.

I think it best to have sessions that persist the browser session itself.
It is nice to come back to working on something without having to
supply a login.

Regards,

Michael
----- Original Message ----- 
From: "Jason E. Stewart" <ja...@op...>
To: <gen...@li...>
Sent: Saturday, May 26, 2001 10:03 AM
Subject: Re: [GeneX-dev] Embperl vs. Mason: Conclusions


> "Jason E. Stewart" <ja...@op...> writes:
> 
> > Right, good point. I was thinking about adding it to the existing
> > timestamp mechanism (using two fields creation_date and
> > modification_date), but I think that's unnecessary. I'll just add
> > modification_date and a trigger to set it on UPDATE.
> 
> Oh, yeah, and we probably want a cron job that wipes out sessions
> older than a certain time frame. What time frame should we use? 7
> days, 14 days?
> 
> jas.
> 
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> http://lists.sourceforge.net/lists/listinfo/genex-dev

Re: [GeneX-dev] Embperl vs. Mason: Conclusions

[Michael P. <mic...@ho...>]

I think it useful to store the login in the session as it permits simple
display (without lookup in the db) for confirmation of who is
logged in. Similarly, keeping the name from the contact list
could be used like this as well. Otherwise, for circumstances
where a login id or a system get shared it can get confusing.

Regard,

Michael Pear
----- Original Message ----- 
From: "Jason E. Stewart" <ja...@op...>
> 
> So how about the following key names for the session hash:
> 
> user_id  => pkey from UserSec
> groups   => list of all groups user belongs to
> 
> Now what about the following:
> 
> login    => login column from UserSec
> password => password column from UserSec
> 
> 
> given user_id, they seem optional and unnecessary to me.
> 
> 
> Comments?
> jas.
> 
> 
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> http://lists.sourceforge.net/lists/listinfo/genex-dev
> 

Re: [GeneX-dev] Embperl vs. Mason: Conclusions

[<ja...@op...>]

"Jason E. Stewart" <ja...@op...> writes:

> Right, good point. I was thinking about adding it to the existing
> timestamp mechanism (using two fields creation_date and
> modification_date), but I think that's unnecessary. I'll just add
> modification_date and a trigger to set it on UPDATE.

Oh, yeah, and we probably want a cron job that wipes out sessions
older than a certain time frame. What time frame should we use? 7
days, 14 days?

jas.

Re: [GeneX-dev] Embperl vs. Mason: Conclusions

[<ja...@op...>]

"Michael Pear" <mic...@ho...> writes:

> This looks simple enough and it bypasses some of the difficulties in
> using Embperl sessions with Postgresql...for some reason that has
> been a difficult problem to resolve. (see
> http://www.mail-archive.com/em...@pe.../msg02301.html
> for example.) It appears that Apache::Session on its own works well
> with Postgresql.
> 
> One suggestion that I have seen on the modperl mailing list is to
> timestamp the session entries. See the message
> http://www.mail-archive.com/mo...@ap.../msg07509.html
> Otherwise, there is no way to clean up old sessions from the
> database reliably.

Right, good point. I was thinking about adding it to the existing
timestamp mechanism (using two fields creation_date and
modification_date), but I think that's unnecessary. I'll just add
modification_date and a trigger to set it on UPDATE.

> Regarding substituting for Embperl sessions, it appears that it
> would be best to just treat GeneX sessions independently and not
> worry whether or not Embperl sessions are on or not and just use the
> Apache::Session directly.

True. I was thinking that if the GeneX session were set automatically
before and page was invoked, and it was set to the default %udat hash,
that would make it easier for scripts. It could also be set to a
different variable altogether, say %genex_session to disambiguate it
from the builtin session system.

> Is there any need for coordination among developers in terms of
> session data?

Sounds like a good idea. 

To make queries efficient we need to track what groups a user belongs
to, that way we can do queries like:

SELECT * FROM ExperimentSet, Security 
WHERE sec_fk = sec_pk AND
      ro_group_fk IN (@group_list)

To automatically filter on groups that are visible to the user. To set
this up we'd need a query like:

SELECT DISTINCT gs_fk FROM GroupLink
WHERE us_fk = $user_id

where $user_id is the primary key from the UserSec table. Keeping
track of $user_id is a good idea as well, because that will enable us
to determine ownership info quickly (Security has the us_fk column
which indicates the owner of the information). Data owners have
permission to modify the security entry for data they own, whereas
members of the rw_group only have permission to modify the *data*
itself, not the permissions on the data.

So how about the following key names for the session hash:

user_id  => pkey from UserSec
groups   => list of all groups user belongs to

Now what about the following:

login    => login column from UserSec
password => password column from UserSec


given user_id, they seem optional and unnecessary to me.


Comments?
jas.

Re: [GeneX-dev] Embperl vs. Mason: Conclusions

[Michael P. <mic...@ho...>]

Jason,

 This looks simple enough and it bypasses some of the difficulties in using Embperl sessions with
Postgresql...for some reason that has been a difficult problem to resolve. (see
http://www.mail-archive.com/em...@pe.../msg02301.html for example.) It appears that
Apache::Session on its own works well with Postgresql.

One suggestion that I have seen on the modperl mailing list is to timestamp the session entries. See
the message  http://www.mail-archive.com/mo...@ap.../msg07509.html Otherwise, there is no way
to clean up old sessions from the database reliably.

Regarding substituting for Embperl sessions, it appears that it would be best to
just treat GeneX sessions independently and not worry whether or not Embperl
sessions are on or not and just use the Apache::Session directly.

Is there any need for coordination among developers in terms of session data?

Regards

Michael Pear

> Hey All,
>
> So after a couple of days I came to the following conclusions:
> * we need a session mechanism that enables storing of user-specific
>   data persistently.
> * whatever session mechanism we use needs to be agnostic: it should
>   work with Empberl, Mason, and straight CGI.
>
> Technologies like Mason and Embperl are very useful, and my feeling is
> that we really don't want to force GeneX users to use only one or the
> other, we should allow each installer to choose which method (if any)
> is prefered.
>
> The solution seems simple: create a GeneX-specific Apache::Session
> mechanism that can be used by all three technologies. It is done, the
> biggest piece of work was ensuring myself that mod_perl was configured
> correctly.
>
> Here's a code snippet for CGI that uses the new mechanism:
>
>    use Bio::Genex::HTMLUtils qw(get_session);
>    use Apache::Registry;
>    use Apache;
>    use vars qw($request);
>
>    $request = Apache->request();
>    my $session = get_session($request);
>    $session->{data} = "Oh what a lucky man I am";
>
> The get_session() method from Bio::GeneX::HTMLUtils does all the work.
> get_session() returns a hash reference that can be used to store any
> user-specific data needed, and it will be stored in the GeneX DB.
>
> It implements the example session code from the Apache::Session man
> page using cookies to pass the session key, and Postgres to store it
> persistantly. To make it work I needed to add a new table, Sessions,
> to the DB that has two fields: a char pkey, and a text data column.
>
> To make this work with Embperl, the following two pieces need to
> happen:
> * default Embperl sessions must be turned off.
> * the above code snippet needs to be added to the initialization code
>   that is run before each page. And then the following can be added:
>
>    %udat = %{$session};
>
> Now when an Embperl page accesses or modifies data in the standard
> %udat hash, it will be accessing the underlying GeneX-specific session
> hash.
>
> Mason doesn't have a default session mechanism, so the above code
> snippet can be added to the top-level handler, and the $session hash
> reference will be available to every component.
>
> Comments?
>
> jas.
>
>
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> http://lists.sourceforge.net/lists/listinfo/genex-dev

[GeneX-dev] Embperl vs. Mason: Conclusions

[<ja...@op...>]

Hey All,

So after a couple of days I came to the following conclusions:
* we need a session mechanism that enables storing of user-specific
  data persistently.
* whatever session mechanism we use needs to be agnostic: it should
  work with Empberl, Mason, and straight CGI.

Technologies like Mason and Embperl are very useful, and my feeling is
that we really don't want to force GeneX users to use only one or the
other, we should allow each installer to choose which method (if any)
is prefered.

The solution seems simple: create a GeneX-specific Apache::Session
mechanism that can be used by all three technologies. It is done, the
biggest piece of work was ensuring myself that mod_perl was configured
correctly. 

Here's a code snippet for CGI that uses the new mechanism:

   use Bio::Genex::HTMLUtils qw(get_session);
   use Apache::Registry;
   use Apache;
   use vars qw($request);
   
   $request = Apache->request();
   my $session = get_session($request);
   $session->{data} = "Oh what a lucky man I am";

The get_session() method from Bio::GeneX::HTMLUtils does all the work.
get_session() returns a hash reference that can be used to store any
user-specific data needed, and it will be stored in the GeneX DB.

It implements the example session code from the Apache::Session man
page using cookies to pass the session key, and Postgres to store it
persistantly. To make it work I needed to add a new table, Sessions,
to the DB that has two fields: a char pkey, and a text data column. 

To make this work with Embperl, the following two pieces need to
happen:
* default Embperl sessions must be turned off.
* the above code snippet needs to be added to the initialization code
  that is run before each page. And then the following can be added:

   %udat = %{$session};

Now when an Embperl page accesses or modifies data in the standard
%udat hash, it will be accessing the underlying GeneX-specific session
hash.

Mason doesn't have a default session mechanism, so the above code
snippet can be added to the top-level handler, and the $session hash
reference will be available to every component.

Comments?

jas.

[GeneX-dev] Re: Finished the installation

[Harry M. <man...@ho...>]

HI Ron,

Sorry for the delay in answering - I just got back to my desk.

That's good news indeed - please let us know how the rest of the testing goes.

And don't forget that you'll help all GeneX testers and developers if you send your GeneX-related comments, questions, etc to the general developers list:

genexdev at SF <gen...@li...>

Cheers
harry


Ron Ophir wrote:
> 
> Dear Harry,
> I am glad to tell you that I finished to install genex successfully. It occur to me that I had two versions of postgres one is 7.0.3 and the other is 7.1. Therefore I uninstall all postgress rpm s and reinstall 7.1. It works.
> Thank you very much for you support
> 
> Ron Ophir, Ph.D.
> DNA Microarray Informatics,
> Biological Services
> Weizmann Istitute of Science
> POB 26
> Rehovot 76100
> Israel
> e-mail: Ron...@we...
> Phone: 972-8-9343456
> Fax:972-8-9344113
> 
>   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> 
>    TEXT.htmName: TEXT.htm
>            Type: Plain Text (text/plain)

-- 
Cheers,
Harry

Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho...

[GeneX-dev] Perl Debugger

[<ja...@op...>]

Hey All, 

One of the reasons I've found perl such a convenient language to
program in is the incredibly powerful debugger that comes built-in to
perl. 

I just found an article at IBM's developerWorks that gives a _really_
useful overview of how to use it. If you program in perl but don't use
perl -d, or even if you do, I would take a look:

http://www-106.ibm.com/developerworks/linux/library/l-pl-deb.html

Cheers,
jas.

Re: [GeneX-dev] Embperl for Session Management

[Michael P. <mic...@ho...>]

There were two things that pointed me towards embperl originally.
1) The simplicity of session management
2) The similarity to other code-embedded-in-html approaches like java server pages and active server
pages
which appeal to me (personal preference) because they separate HTML design
 from program design.

I didn't undertake any comparison with other options, so this wasn't a choice made from thorough
investigation, but rather from immediate necessity, especially regarding sessions.

Embperl (as you mentioned  in a later message) does use Apache::Session underneath.
I imagine that it would be possible to use that data from other scripts through Apache::Session,
but has that draw back that potentially session data could be corrupted if some other program
decided to try to persist something differently.

Either way, whomever develops code relying on sessions will need to adhere to some conventions
if they are adding anything that is managed through sessions...embperl provides such a standard, so
it
is attractive from that point of view.

I think what we certainly see is that there are some concrete requirements (e.g., session
management)
and other things that are personal preferences (e.g., embedded code vs. embedded html) The former
are the easy ones to satisfy....the latter are the more difficult religious issues :-)

Regards,

Michael Pear
----- Original Message -----
From: "Jason E. Stewart" <ja...@op...>
To: <gen...@li...>
Sent: Thursday, May 24, 2001 9:22 AM
Subject: [GeneX-dev] Embperl for Session Management


> Hey All,
>
> I've been using Michael Pear's code to handle user login and session
> management, and I have some concerns that I'd like to discuss.
>
> They are not major issues, merely philosophical ones.
>
> Embperl provides two separate features:
> * session management: Through use of cookies it remembers who you are
>   and can persistently store any information you wish between http
>   requests.
> * Perl code embedded in HTML: It seems that Embperl prefers that you
>   look at the world as primarily HTML, and make the content of the WWW
>   pages dynamic by embedding code within bits of static HTML.
>
> Here are my concerns:
> * the session management is fairly well obscured. One one hand this is
>   convenient for writing applications using embperl because all the
>   work is handled under the hood. But it also means you *have* to use
>   embperl to get at the session info.
> * The current WWW scripts distributed with GeneX are CGI scripts that
>   have bits of HTML embedded within them, and not visa versa.
>
> My central concern with using Embperl is that in order to access
> session information created by Embperl you have to write tools using
> embperl. If we could have a more centralized WWW session management
> that is usable by standalone CGI, as well as Embperl, as well as say
> HTML::Mason, I would be happier.
>
> Also, my coding style really favors the code with embedded HTML and
> not the other way around, so I would like the flexibility of doing
> both. I believe that embperl comes with a mechanism for executing CGI
> scripts, but I have not used it.
>
> All in all, I think use of embperl is a big win, I would like to make
> it's use slightly more flexible within GeneX so that we don't
> eliminate potential contributors, because they want to make standalone
> scripts and not use embperl.
>
> Feedback?
> jas.
>
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> http://lists.sourceforge.net/lists/listinfo/genex-dev

[GeneX-dev] Re: Debian package for GeneX?

[<ja...@op...>]

Hey Tony,

A reasonable question, so I took the liberty of making my answer
public. 

A debian package would be really valuable I feel. It would mean that
people could simply say:
  apt-get install genex

And it would download genex *and all it's prerequisites* over the
internet, configure and install them.

When Harry and I stopped major development on the installer
application, we realized that it needed to move to some sort of GUI
for interactive configuration. I think that debconf might be what we
need. 

The issue is:
* GeneX needs a *lot* of configuration input from the user
* whatever configuration tool we develop needs to work on all linux
  systems (not just debian), and other Unix systems as well (and
  perhaps even Windows??).

That led us to believe that we wanted a WWW based installer that would
be independant of OS.

As long as we could do that under debian, I would be happy to make it
a package.

jas.

"A.J. Rossini" <ro...@bl...> writes:

> BTW, have you given thought to a debian package for GeneX?

Re: [GeneX-dev] Embperl for Session Management

[<ja...@op...>]

"Jason E. Stewart" <ja...@op...> writes:

> All in all, I think use of embperl is a big win, I would like to make
> it's use slightly more flexible within GeneX so that we don't
> eliminate potential contributors, because they want to make standalone
> scripts and not use embperl.

I found a great thread in the mod_perl mailing list discussing the
pros and cons of Embperl and Mason:

http://www.davin.ottawa.on.ca/archive/modperl/1999-07/msg00909.phtml

Jon Swartz, the author of Mason, pointed out his philosophy:

  My general philosophy for Mason is to add only features that have no
  equivalent elsewhere in Perl/mod_perl/CPAN, and when features do
  exist elsewhere, to encourage people to use their native syntax and
  interfaces.  This lets me spend a little more time and energy on
  unique features.  In contrast, Embperl spends some amount of energy
  on syntactic shortcuts: its own for/while/if constructs, dynamic
  tables, sessions, database access, etc. Some of these are quite
  nice. I'm not claiming my philosophy is better; it just jibes more
  with my coding style. Similarly each user's choice of package may be
  based as much on style as on supported features.

This makes a lot of sense to me. I'd like to hear what others feel.

Jon, also pointed out that session management in Mason is available
directly through Apache::Session, which is what Embperl uses, but puts
it's own wrapper around it (thus make it simpler to use, but
inaccessible to other modules). I think the direct use of
Apache::Session sounds very flexible, and any one could write their
own scripts to access the session info without needing to use Mason at
all, which I think will help people contribute more code to GeneX in
the long run.

$0.05,
jas.

[GeneX-dev] Embperl for Session Management

[<ja...@op...>]

Hey All,

I've been using Michael Pear's code to handle user login and session
management, and I have some concerns that I'd like to discuss. 

They are not major issues, merely philosophical ones.

Embperl provides two separate features:
* session management: Through use of cookies it remembers who you are
  and can persistently store any information you wish between http
  requests. 
* Perl code embedded in HTML: It seems that Embperl prefers that you
  look at the world as primarily HTML, and make the content of the WWW
  pages dynamic by embedding code within bits of static HTML.

Here are my concerns:
* the session management is fairly well obscured. One one hand this is
  convenient for writing applications using embperl because all the
  work is handled under the hood. But it also means you *have* to use
  embperl to get at the session info. 
* The current WWW scripts distributed with GeneX are CGI scripts that
  have bits of HTML embedded within them, and not visa versa.

My central concern with using Embperl is that in order to access
session information created by Embperl you have to write tools using
embperl. If we could have a more centralized WWW session management
that is usable by standalone CGI, as well as Embperl, as well as say
HTML::Mason, I would be happier.

Also, my coding style really favors the code with embedded HTML and
not the other way around, so I would like the flexibility of doing
both. I believe that embperl comes with a mechanism for executing CGI
scripts, but I have not used it.

All in all, I think use of embperl is a big win, I would like to make
it's use slightly more flexible within GeneX so that we don't
eliminate potential contributors, because they want to make standalone
scripts and not use embperl.

Feedback?
jas.

Re: [GeneX-dev] Diagram of workflow for OMG

[Bill B. <wd...@nc...>]

Actually I mean the software developer / biologist  fence.  Steve has
represented a lab process in software development terms.

-bill

ps  I'll plan to come to your place.  What was your address?


----- Original Message -----
From: "Jason E. Stewart" <ja...@op...>
To: <gen...@li...>
Sent: Thursday, May 24, 2001 8:47 AM
Subject: Re: [GeneX-dev] Diagram of workflow for OMG


> "Bill Beavis" <wd...@nc...> writes:
>
> > Looks like communication on both sides of the fence.  Maybe the fence
will
> > continue to come down.
>
> Hey Bill,
>
> Do you mean the Affy fence? or the OMG fence?
>
> If Affy, after a lot of pressure to get someone from affy involved (to no
> avail), Steve Chervitz volunteered completely independently. He's only
> been to one meeting so far, but has picked up quickly.
>
> If OMG, I'm not sure what you mean.
>
> jas.
>
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> http://lists.sourceforge.net/lists/listinfo/genex-dev
>

Re: [GeneX-dev] Diagram of workflow for OMG

[<ja...@op...>]

"Bill Beavis" <wd...@nc...> writes:

> Looks like communication on both sides of the fence.  Maybe the fence will
> continue to come down.

Hey Bill,

Do you mean the Affy fence? or the OMG fence? 

If Affy, after a lot of pressure to get someone from affy involved (to no
avail), Steve Chervitz volunteered completely independently. He's only
been to one meeting so far, but has picked up quickly.

If OMG, I'm not sure what you mean.

jas.

Re: [GeneX-dev] Diagram of workflow for OMG

[Bill B. <wd...@nc...>]

Looks like communication on both sides of the fence.  Maybe the fence will
continue to come down.

-wdb

----- Original Message -----
From: "Jason E. Stewart" <ja...@op...>
To: <gen...@li...>
Sent: Wednesday, May 23, 2001 6:36 PM
Subject: [GeneX-dev] Diagram of workflow for OMG


> Hey All,
>
> Here is a nice little diagram from Steve Chervitz of Affymetrix that
> introduces some of the nomenclature that we've been working on in the
> OMG working group on Gene Expression. It shows the workflow model of
> how an array is hybridized, etc. and eventually how data is produced.
>
> For your enjoyment,
> jas.
>
>

[GeneX-dev] Re: CyberT

[Tony L. <td...@uc...>]

You could rewrite the code using some sort of power-law.  But I think 
most flavors of the power law would result in errors being Gaussian 
on a log scale....

At 8:12 AM -0700 5/22/01, Harry Mangalam wrote:
>Illes J FARKAS wrote:
>>
>>  On Mon, 21 May 2001, Harry Mangalam wrote:
>>
>>  > Date: Mon, 21 May 2001 20:08:12 -0700
>>  > From: Harry Mangalam <man...@ho...>
>>  > To: fi...@el...
>>  > Cc: wd...@nc..., genexdev at SF <gen...@li...>
>>  > Subject: Re: Cyber-T all-in-one
>>
>>  > Please let us know if you need help in installing the system.  I'll be
>>  on the road for the rest of the week, but the other GeneX developers will
>>  help. as long as you post to:
>>  >
>>  > gen...@li...
>>
>>  Thank you for the answer,
>>
>>  1) If I'm not mistaken, the Cyber-T software assumes that the distribution
>>  of data points (for one gene) is normal (i.e., Gaussian).
>
>As written, that's right.
>
>>  Or is it possible to use a power-law, for instance?
>
>If you wanted to use a power law, you'd have to re-write some of the 
>R library I think - Tony, could you comment?
>
>>  2) To use the paired data analysis page (for cy3/cy5) do I have to compute
>>  the Paired Expression Value Column? It seems to me that this column
>>  contains no information beyond the measured values, but it is simply a
>>  function of the measured control and data values.
>
>You have to compute this ONLY if you want the benefit of the 
>Bayesian analysis.
>It IS a function of the measured control and data values, but that 
>is what the Bayesian prior operates on.
>
>>
>>  Thank you for your help in advance.
>>
>>  Best,
>>  Illes Farkas
>>
>>  --
>>  Illes J FARKAS
>>  http://angel.elte.hu/~fij
>
>--
>Cheers,
>Harry
>
>Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho...

-- 

Tony Long

Ecology and Evolutionary Biology
Steinhaus Hall
University of California at Irvine
Irvine, CA
92697-2525

Tel:  (949) 824-2562   (office)
Tel:  (949) 824-5994   (lab)
Fax: (949) 824-2181

email:  td...@uc...
http://hjmuller.bio.uci.edu/~labhome/

[GeneX-dev] Re: CyberT

[Harry M. <man...@ho...>]

Illes J FARKAS wrote:
> 
> On Mon, 21 May 2001, Harry Mangalam wrote:
> 
> > Date: Mon, 21 May 2001 20:08:12 -0700
> > From: Harry Mangalam <man...@ho...>
> > To: fi...@el...
> > Cc: wd...@nc..., genexdev at SF <gen...@li...>
> > Subject: Re: Cyber-T all-in-one
> 
> > Please let us know if you need help in installing the system.  I'll be
> on the road for the rest of the week, but the other GeneX developers will
> help. as long as you post to:
> >
> > gen...@li...
> 
> Thank you for the answer,
> 
> 1) If I'm not mistaken, the Cyber-T software assumes that the distribution
> of data points (for one gene) is normal (i.e., Gaussian). 

As written, that's right.

> Or is it possible to use a power-law, for instance?

If you wanted to use a power law, you'd have to re-write some of the R library I think - Tony, could you comment?

> 2) To use the paired data analysis page (for cy3/cy5) do I have to compute
> the Paired Expression Value Column? It seems to me that this column
> contains no information beyond the measured values, but it is simply a
> function of the measured control and data values.

You have to compute this ONLY if you want the benefit of the Bayesian analysis.
It IS a function of the measured control and data values, but that is what the Bayesian prior operates on.

> 
> Thank you for your help in advance.
> 
> Best,
> Illes Farkas
> 
> --
> Illes J FARKAS
> http://angel.elte.hu/~fij

-- 
Cheers,
Harry

Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho...

[GeneX-dev] (no subject)

[Illes J F. <fi...@ha...>]

On Mon, 21 May 2001, Harry Mangalam wrote:

> Date: Mon, 21 May 2001 20:08:12 -0700
> From: Harry Mangalam <man...@ho...>
> To: fi...@el...
> Cc: wd...@nc..., genexdev at SF <gen...@li...>
> Subject: Re: Cyber-T all-in-one

> Please let us know if you need help in installing the system.  I'll be
on the road for the rest of the week, but the other GeneX developers will
help. as long as you post to:   
> 
> gen...@li...



Thank you for the answer,

1) If I'm not mistaken, the Cyber-T software assumes that the distribution
of data points (for one gene) is normal (i.e., Gaussian). Or is it
possible to use a power-law, for instance?

2) To use the paired data analysis page (for cy3/cy5) do I have to compute
the Paired Expression Value Column? It seems to me that this column
contains no information beyond the measured values, but it is simply a
function of the measured control and data values. 


Thank you for your help in advance.

Best,
Illes Farkas

-- 
Illes J FARKAS
http://angel.elte.hu/~fij

[GeneX-dev] Re: Cyber-T all-in-one

[Harry M. <man...@ho...>]

Hi Illes,

No, I'm afraid not, at least at this point.  For the next version we hope to have an easier installation procedure, but since the GeneX server depends on so many external packages, we still require
you to install them yourself.  However, the installation procedure is pretty straightforward.  The hardest part is installing and configuring the Postgres database, but if you use RedHat's RPM or the
Debian dselect/apt-get procedures (we particularly like Debian), eevn this is not particularly hard.  The bulk of the required utilities are either standard or optional parts of most Linux
Distributions so it's just a matter of typing:

rpm -i the.package.name.rpm  [on Redhat]

or 

apt-get install the.package.name [on Debian]

Installing it on another unix (SOlaris, IRIX, HPUX) would be more difficult because you'd have to replace a lot of the supplied utils with the GNU (superior) equivalents which are the defaults on a
Linux system.

The only thing that remains is to upgrade the required Perl modules, most of which can be installed very easily via the Perl CPAN shell (as described in the INSTALL file) and you're off to the [GeneX]
races.

It might be possible to write a Debian 'deb' package that describes the dependencies of teh GeneX system and instructs the installer to get all the missing bits, but for until we have more time to
work on the installer, we're going to spend most of our time on the basic functionality and data.

Thanks very much for writing to us tho, we take your suggestions to heart and I personally would be much more willing to try something if it conformed to the normal 'autoconf' procedure that you
describe:

./configure; make; make install;

Please let us know if you need help in installing the system.  I'll be on the road for the rest of the week, but the other GeneX developers will help. as long as you post to:

gen...@li...


Cheers
harry


Illes J FARKAS wrote:
> 
> To: hj...@nc...
> Cc: wd...@nc...
> 
> Dear Dr. Mangalam,
> 
> I have visited the Cyber-T website and also downloaded the package
> GeneX-Server-1.0.2.tar.gz, since I hope to install it locally.
> 
> Do you happen to have an "all-in-one" package for this server, where
> installation can be carried out just by saying [as root] a
> few words as 'make install; make; configure;' ?
> 
> Thank you very much in advance,
> Illes Farkas
> 
> --
> Illes J FARKAS
> http://angel.elte.hu/~fij

-- 
Cheers,
Harry

Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho...

[GeneX-dev] Re: Finished the installation (run time error)

[Harry M. <man...@ho...>]

Ron Ophir wrote:
> 
> Dear Harry,
> Thank you very much for your help. I beilive I finished the installation. However, when I checked the link "Database Query", which runs query_intro.pl I got the following error message:
> 
> Died at /usr/local/lib/perl5/Bio/Genex/DBUtils.pm line 1015
> 
> is it because my database is empty?

Hmmmmm.... Did you initialize the DB with the script that was at:

http://genebox.ncgr.org/genex/download/DB/genex-initdb-latest.gz

However, if you got thru the installation process, you must have instantiated some version of the database (or fooled the installer :) )

And it looks like you did get it installed as I can peek at the installation from here (and see that you do have a working DB):

http://linux-104.weizmann.ac.il/genex/analysis_tools.shtml

From the DB status page, it looks like things are as they should be, but there's one thing we didn't put on there that we probably should have:  what version fo PostgreSQL are you using?  It should be
version 7 or greater; if it's < 7, I remember that there were some problems that eventually required that we move to 7.


Jason:  can you tell if this is a Postgres version problem?



> Here attached the lines from DBUtils.pm including 1015:
> 
>    1010   # finally get the species of that sequence feature
>    1011   $sql = create_select_sql($dbh,COLUMNS=>['spc_fk'],
>    1012                            FROM=>['UserSequenceFeature'],
>    1013                            WHERE=>"usf_pk = $usf_fk",
>    1014                           );
>    1015   my $spc_fk = ($dbh->selectrow_array($sql))[0] || die $DBI::errstr;
>    1016   require Bio::Genex::Species;
>    1017   return Bio::Genex::Species->new(id=>$spc_fk);
>    1018 }
> 
> Thank you in advance,
> 
> Ron Ophir, Ph.D.
> DNA Microarray Informatics,
> Biological Services
> Weizmann Istitute of Science
> POB 26
> Rehovot 76100
> Israel
> e-mail: Ron...@we...
> Phone: 972-8-9343456
> Fax:972-8-9344113
> 
>   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>                Name: TEXT.htm
>    TEXT.htm    Type: Hypertext Markup Language (TEXT/HTML)
>            Encoding: base64

-- 
Cheers,
Harry

Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho...

Re: [GeneX-dev] Re: GeneX listservs and help

[<ja...@op...>]

"Todd Peterson" <tf...@nc...> writes:

> Don't know the server code hardly at all so it would be ignorant of
> me to say how easy or hard it would be. Depends on how much Unix
> specific stuff is in the code and how faithfully cygwin reproduces
> the behavior.

This was a common question at the two talks I gave at the Hutch and
Institute for Systems Biology on Friday. At first I wanted to say:
"Forget it!!" But then I realized if people wanted to spend some time
checking it out, so much the better for us.

With cygwin it should work out of the box. Without cygwin, I'm pretty
sure it can be made to work with a relatively small amount of work.

AFAIK the most significant unix dependent piece is the install-all
script. I also believe that the cybert stuff uses unix system specific
stuff to write files. I know that install-all could be shifted to use
OS independant file operations with very little work (just use all the
Perl installation stuff). CyberT should also be easy, but will
probably take a bit of digging since the code that interacts with the
file system is scattered around a bit.

jas.

> ----- Original Message -----
> From: "Harry Mangalam" <hj...@nc...>
> To: "Todd Peterson" <tf...@nc...>
> Cc: <gen...@li...>; <adl...@uc...>
> Sent: Thursday, May 17, 2001 11:04 AM
> Subject: [GeneX-dev] Re: GeneX listservs and help
> 
> 
> > Well Well well... Then it might mean that we could get GeneX
> > running on NT/2k as well?  Have to think about this, but it might
> > be possible, tho still aesthetically ugly... ;)
> >
> > if apache and cygwin are ok, and you can implement the genex bits
> > on the cygwin side (so paths, permissions, system calls etcare
> > handled the linux way, then I guess there's no reason that it
> > couldn't work.  R has a win port (or probably better to run the
> > Cygwin Linux port)

[GeneX-dev] Re: GeneX installation troubleshoot

[Harry M. <man...@ho...>]

Ron Ophir wrote:

> > I couldn't find dtd2html at the URL specified in the script?
> =

> It should be in the same directory as the GeneX-Server:
> =

> http://genebox.ncgr.org/download/genex-server/perlSGML.2001Jan23.tar.gz=

> =

> **This worked !! thanks!!

OK, one thing down.


> **Addressing to these links I couldn't download the entire package succ=
esfully. The connection always broke down even if I used the multiple fil=
e option.
> **I manage to download the zip file (not the rpm) of jre1.3 however the=
 installation documentation instruct me to put me the unziped package und=
er /usr/local/java and so I **did. I gave this path once and once /usr/lo=
cal/java/bin/i386/green_threads/,  in the ISA but still it couldn't find =
it.



http://www-106.ibm.com/developerworks/java/jdk/linux130/jre-info.html
go to the download section, register if you havevn't yet, and try it from=
 there.

There's often net congestion, so you might try it today if you can.  From=
 here, it's not super-speedy, but I'm getting decent speed.

and the following one should have been printed to your screen if it faile=
d to find jar in the 1st place).

http://java.sun.com/j2se/1.3/docs/api/java/util/jar/package-summary.html

If you just can't get it to install properly (the zip file may be the win=
dows version), then the other way of getting around this problem for now =
is to ignore it or edit the install-all.pl file and
comment out the line (~223) that looks like:

jar =3D> 'http://java.sun.com/j2se/1.3/docs/api/java/util/jar/package-sum=
mary.html',

It also looks like your PATH doesn't include the java/bin directory where=
 you installed it.   =


PATH =3D /usr/local/sbin:/usr/sbin:/sbin:/usr/local/bin:/usr/local/sbin: =
\                      /sbin:/usr/sbin:/bin:/usr/bin:/usr/X11R6/bin:/root=
/bin

you probably have to add:

:/usr/local/java/bin

to the end of yor PATH string, either by adding it to your shell environm=
ent PATH or explicitly creating one for the installation (line ~240) by c=
ommenting out the line:

   PATH     =3D>  $ENV{PATH},	# if this is too liberal, comment this line=
 =

                                # and use the next one

and UNcommenting the line beneath it, setting the PATH explicitly

#  PATH    =3D>  '/bin:/usr/bin:/usr/local/bin:/usr/bin/X11:/home/genex/b=
in:/usr/lib:/usr/local/lib',

 =

> **In addition from some reason the ISA couldn't find xgvis. It finds xg=
obi but not xgvis. =


That's odd; it should be installed in the same place as xgobi, but don't =
worry about xgvis yet.  It's not used directly yet.  Did you install xgob=
i and install both xgobi and xgvis in the same place?


> **In order to help you to help me I include the following information (=
the Option.Reminder file; find on xgvis; path list of java directory) :

THANKS!  This is helpful!

It looks like it found NEITHER xgobi nor xgvis..


> ** Option.Reminder
> Following are the Directory and URLs you set or allowed to be set:
> CGIDIR =3D /var/www/cgi-bin
> CGITMPDIR =3D /tmp/genex
> CGITMPURL =3D http://linux-104.weizmann.ac.il/genex/tmp
> CGI_ROOT_URL =3D http://linux-104.weizmann.ac.il/cgi-bin
> CONTACT_EMAIL =3D ron...@we...
> CURA_TOOL =3D genex/curation-tool
> CYBERT_DIR =3D genex/cybert
> CyberT_Demo_DIR =3D genex/CyberT-Demo
> DB_NAME =3D genex
> DOWNLOAD_DIR =3D genex/download
> DTD2HTML =3D /usr/local/bin/dtd2html
> DTD_DIR =3D genex/DTD
> DTD_HTML_DIR =3D /usr/local/genex/lib/dtd/genexml-html
> DTD_HTML_URL =3D http://linux-104.weizmann.ac.il/genex/DTD/genexml-html=

> ENV_HOME =3D /tmp/genex
> GENEXML_DIR =3D /usr/local/genex/lib/dtd
> GENEXML_URL =3D http://linux-104.weizmann.ac.il/genex/DTD
> GENEX_CACHE_DIR =3D /usr/local/genex/cache
> GENEX_CB_CACHE_DIR =3D /usr/local/genex/cache/db2xml/cb
> GENEX_CGIDIR =3D /var/www/cgi-bin/genex
> GENEX_CGI_URL =3D http://linux-104.weizmann.ac.il/cgi-bin/genex
> GENEX_CONNECT =3D $Bio::Genex::LOCAL =3D 1;
> GENEX_CURATOR =3D shi...@we...
> GENEX_CUR_TOOL_DIR =3D /var/www/cgi-bin/genex/curation-tool
> GENEX_DBMS =3D Pg
> GENEX_DB_USERSEC =3D geL8TEYU5FBEI
> GENEX_DIR =3D genex
> GENEX_EXAMPLE_DIR =3D /var/www/cgi-bin/genex/samples
> GENEX_EXP_CACHE_DIR =3D /usr/local/genex/cache/db2xml/exp
> GENEX_EXTRALIBS =3D use lib q[/usr/local/lib/perl5];
> use lib q[/usr/local/lib/perl5];
> =

> GENEX_GRAPHICS_URL =3D http://linux-104.weizmann.ac.il/genex/graphics
> GENEX_HOST =3D localhost
> GENEX_HTM_URL =3D http://linux-104.weizmann.ac.il/genex
> GENEX_INSTALLSITE =3D /usr/local/lib/perl5
> GENEX_LOCAL =3D 1
> GENEX_MAN1 =3D /usr/local/genex/man/man1
> GENEX_MAN3 =3D /usr/local/genex/man/man3
> GENEX_PORT =3D 5432
> GENEX_QUERY_DIR =3D /var/www/cgi-bin/genex/gxquery
> GENEX_RO_PASSWORD =3D
> GENEX_RO_USER =3D readonly
> GENEX_SECRET =3D Sun May 20 15:03:54 2001
> GENEX_SERVER_INSTALLED_BY =3D ron...@we...
> GENEX_SUBMISSION_HOME =3D /usr/local/genex/submission
> GENEX_SU_PASSWORD =3D
> GENEX_SU_USER =3D genex
> GENEX_URL_CUR_TOOL =3D http://linux-104.weizmann.ac.il/cgi-bin/genex/cu=
ration-tool
> GENEX_URL_EXAMPLE =3D http://linux-104.weizmann.ac.il/cgi-bin/genex/sam=
ples
> GENEX_URL_QUERY =3D http://linux-104.weizmann.ac.il/cgi-bin/genex/gxque=
ry
> GNUCUT =3D /bin/cut
> GNUINSTALL =3D /usr/bin/install
> GNUMKDIR =3D /bin/mkdir
> GNUPLOT =3D /usr/bin/gnuplot
> GNUSORT =3D /bin/sort
> GNUTAIL =3D /usr/bin/tail
> GNUTAR =3D /bin/tar
> GRAPHICS_DIR =3D genex/graphics
> GS =3D /usr/bin/gs
> GXQUERY_DIR =3D genex/gxquery
> HTMLDIR =3D /var/www/html
> HTMLTMPDIR =3D /var/www/html/genex/tmp
> HTML_ROOT_URL =3D http://linux-104.weizmann.ac.il
> HTTP_ERR_LOG =3D /var/log/httpd/error_log
> INCLUDE_DIR =3D genex/include
> JAR =3D
> LOCAL_BIN =3D /usr/local/genex/bin
> LOCAL_LIB =3D /usr/local/genex/lib
> LOCAL_ROOT =3D /usr/local/genex
> LOCAL_SHARE =3D /usr/local/genex/share
> LOCAL_VAR =3D /usr/local/genex/var
> LOGIN_DIR =3D genex/login
> MAX_SYSTMP_SIZE =3D 15
> MAX_TMPFILE_AGE =3D 24
> MERGEM_DIR =3D genex/mergem
> MPAGE =3D /usr/bin/mpage
> PATH =3D /usr/local/sbin:/usr/sbin:/sbin:/usr/local/bin:/usr/local/sbin=
:/sbin:/usr/sbin:/bin:/usr/bin:/usr/X11R6/bin:/root/bin
> PREFIX =3D /usr/local/lib/perl5
> R =3D /usr/bin/R
> RCLUSTER_PERL_LIB =3D /usr/local/lib/perl5/RCluster
> RCLUST_DIR =3D genex/rcluster
> RCluster_Demo_DIR =3D genex/RCluster-Demo
> R_VERSION =3D R 1.2.3 (2001-04-26).
> SENDMAIL =3D /usr/sbin/sendmail
> START_PERL =3D #!/usr/local/bin/perl
> SYSTMP =3D /tmp/genex
> TOP_LEVEL_DIR =3D genex/top_level
> VERSION_STRING =3D $Id: install-all.pl,v 1.82 2001/03/02 19:23:13 jes E=
xp $
> VNCSERVER =3D /usr/bin/vncserver
> WWWHOST =3D linux-104.weizmann.ac.il
> XCLUSTER =3D
> XCLUSTER_DIR =3D genex/xcluster
> XGOBI =3D
> XGOBID =3D /usr/local/src/xgobi
> XGVIS =3D
> XML_WRITER =3D /usr/local/genex/bin/db2xml.pl
> =

> Following are the Application Paths you set or allowed to be set:
> R =3D /usr/bin/R
> cut =3D /bin/cut
> dtd2html =3D /usr/local/bin/dtd2html
> gnuplot =3D /usr/bin/gnuplot
> gs =3D /usr/bin/gs
> install =3D /usr/bin/install
> jar =3D
> mkdir =3D /bin/mkdir
> mpage =3D /usr/bin/mpage
> sendmail =3D /usr/sbin/sendmail
> sort =3D /bin/sort
> tail =3D /usr/bin/tail
> tar =3D /bin/tar
> vncserver =3D /usr/bin/vncserver
> xcluster =3D
> xgobi =3D
> xgvis =3D
> =

> Following are the ENVIRONMENT VARIABLES you set or allowed to be set:
> ENV_HOME =3D /tmp/genex
> PATH =3D /usr/local/sbin:/usr/sbin:/sbin:/usr/local/bin:/usr/local/sbin=
:/sbin:/usr/sbin:/bin:/usr/bin:/usr/X11R6/bin:/root/bin
> XGOBID =3D /usr/local/src/xgobi
> =

> **Find on xgvis
> =

> /usr/local/lib/R/library/xgobi/help/xgvis
> /usr/local/src/xgobi/src/xgvis
> /usr/local/src/xgobi/help/xgvis
> /usr/local/genex/lib/R/library/xgobi/help/xgvis
> =

> **List path of java ( where I put the jre 1.3)
> =

> /usr/local/java/:
> =AF----------------CHANGES
> =AF----------------ControlPanel.html
> =AF----------------COPYRIGHT
> =AF----------------LICENSE
> =AF----------------LICENSE.fr
> =AF----------------README
> =AF---------------Welcome.html
> =3D=3D=3D=3D=3D=3D=3D=3D=3D/bin:
> =AF--------------------awt_robot*
> =AF--------------------ControlPanel*
> =3D=3D=3D=3D=3D=3D=3D=3D=3Di386/
> =AF-------------------java@
> =AF-------------------keytool@
> =AF-------------------policytool@
> =AF-------------------realpath*
> =AF-------------------rmid@
> =AF-------------------rmiregistry@
> =AF-------------------tnameserv@
> =

> /usr/local/java/bin/i386:
> =AF-------------------green_threads/
> =AF-------------------native_threads/
> =AF-------------------realpath*
> =

> /usr/local/java/bin/i386/green_threads:
> =AF--------------------------------------------appletviewer*
> =AF--------------------------------------------extcheck*
> =AF--------------------------------------------idlj*
> =AF--------------------------------------------jar*
> =AF--------------------------------------------jarsigner*
> =AF--------------------------------------------java*
> =AF--------------------------------------------javac*
> =AF--------------------------------------------javadoc*
> =AF--------------------------------------------javah*
> =AF--------------------------------------------javap*
> =AF--------------------------------------------jdb*
> =AF--------------------------------------------keytool*
> =AF--------------------------------------------native2ascii*
> =AF--------------------------------------------oldjava*
> =AF--------------------------------------------oldjavac*
> =AF--------------------------------------------oldjdb*
> =AF--------------------------------------------policytool*
> =AF--------------------------------------------rmic*
> =AF--------------------------------------------rmid*
> =AF--------------------------------------------rmiregistry*
> =AF--------------------------------------------serialver*
> =AF--------------------------------------------tnameserv*
> =

> /usr/local/java/bin/i386/native_threads:
> =AF--------------------------------------------java*
> =AF--------------------------------------------java_vm*
> =AF--------------------------------------------keytool*
> =AF--------------------------------------------policytool*
> =AF--------------------------------------------rmid*
> =AF--------------------------------------------rmiregistry*
> =AF--------------------------------------------tnameserv*
> =

> /usr/local/java/lib:
> ----------------applet/
> -----------------audio/
> -----------------cmm/
> content-types.properties
> =AF----------------ext/
> flavormap.properties
> font.properties
> font.properties.ja
> font.properties.zh
> fonts/
> i18n.jar
> i386/
> images/
> javaplugin.jar
> jvm.cfg
> jvm.hprof.txt
> jvm.jcov.txt
> locale/
> psfontj2d.properties
> psfont.properties.ja
> rt.jar
> security/
> sunrsasign.jar
> tzmappings
> =

> /usr/local/java/lib/applet:
> =

> /usr/local/java/lib/audio:
> soundbank.gm
> =

> /usr/local/java/lib/cmm:
> CIEXYZ.pf
> GRAY.pf
> LINEAR_RGB.pf
> PYCC.pf
> sRGB.pf
> =

> /usr/local/java/lib/ext:
> =

> /usr/local/java/lib/fonts:
> fonts.dir
> LucidaBrightDemiBold.ttf
> LucidaBrightDemiItalic.ttf
> LucidaBrightItalic.ttf
> LucidaBrightRegular.ttf
> LucidaSansDemiBold.ttf
> LucidaSansDemiOblique.ttf
> LucidaSansOblique.ttf
> LucidaSansRegular.ttf
> LucidaTypewriterBoldOblique.ttf
> LucidaTypewriterBold.ttf
> LucidaTypewriterOblique.ttf
> LucidaTypewriterRegular.ttf
> =

> /usr/local/java/lib/i386:
> classic/
> client/
> green_threads/
> hotspot@
> libagent.so*
> libawt.so*
> libcmm.so*
> libdcpr.so*
> libfontmanager.so*
> libhprof.so*
> libioser12.so*
> libjavaplugin_jni.so*
> libjava.so*
> libjawt.so*
> libjcov.so*
> libJdbcOdbc.so*
> libjpeg.so*
> libjsound.so*
> libmlib_image.so*
> libnet.so*
> libpreemptive_close.so*
> libverify.so*
> libzip.so*
> native_threads/
> server/
> =

> /usr/local/java/lib/i386/classic:
> libjvm.so*
> Xusage.txt
> =

> /usr/local/java/lib/i386/client:
> libjvm.so*
> Xusage.txt
> =

> /usr/local/java/lib/i386/green_threads:
> libhpi.so*
> =

> /usr/local/java/lib/i386/native_threads:
> libhpi.so*
> =

> /usr/local/java/lib/i386/server:
> libjvm.so*
> Xusage.txt
> =

> /usr/local/java/lib/images:
> cursors/
> =

> /usr/local/java/lib/images/cursors:
> cursors.properties
> invalid32x32.gif
> motif_CopyDrop32x32.gif
> motif_CopyNoDrop32x32.gif
> motif_LinkDrop32x32.gif
> motif_LinkNoDrop32x32.gif
> motif_MoveDrop32x32.gif
> motif_MoveNoDrop32x32.gif
> =

> /usr/local/java/lib/locale:
> de/
> es/
> fr/
> it/
> ja/
> ko/
> ko.UTF-8/
> sv/
> zh/
> zh.GBK/
> zh_TW/
> zh_TW.BIG5/
> =

> /usr/local/java/lib/locale/de:
> LC_MESSAGES/
> =

> /usr/local/java/lib/locale/de/LC_MESSAGES:
> sunw_java_plugin.mo
> =

> /usr/local/java/lib/locale/es:
> LC_MESSAGES/
> =

> /usr/local/java/lib/locale/es/LC_MESSAGES:
> sunw_java_plugin.mo
> =

> /usr/local/java/lib/locale/fr:
> LC_MESSAGES/
> =

> /usr/local/java/lib/locale/fr/LC_MESSAGES:
> sunw_java_plugin.mo
> =

> /usr/local/java/lib/locale/it:
> LC_MESSAGES/
> =

> /usr/local/java/lib/locale/it/LC_MESSAGES:
> sunw_java_plugin.mo
> =

> /usr/local/java/lib/locale/ja:
> LC_MESSAGES/
> =

> /usr/local/java/lib/locale/ja/LC_MESSAGES:
> sunw_java_plugin.mo
> =

> /usr/local/java/lib/locale/ko:
> LC_MESSAGES/
> =

> /usr/local/java/lib/locale/ko/LC_MESSAGES:
> sunw_java_plugin.mo
> =

> /usr/local/java/lib/locale/ko.UTF-8:
> LC_MESSAGES/
> =

> /usr/local/java/lib/locale/ko.UTF-8/LC_MESSAGES:
> sunw_java_plugin.mo
> =

> /usr/local/java/lib/locale/sv:
> LC_MESSAGES/
> =

> /usr/local/java/lib/locale/sv/LC_MESSAGES:
> sunw_java_plugin.mo
> =

> /usr/local/java/lib/locale/zh:
> LC_MESSAGES/
> =

> /usr/local/java/lib/locale/zh/LC_MESSAGES:
> sunw_java_plugin.mo
> =

> /usr/local/java/lib/locale/zh.GBK:
> LC_MESSAGES/
> =

> /usr/local/java/lib/locale/zh.GBK/LC_MESSAGES:
> sunw_java_plugin.mo
> =

> /usr/local/java/lib/locale/zh_TW:
> LC_MESSAGES/
> =

> /usr/local/java/lib/locale/zh_TW/LC_MESSAGES:
> sunw_java_plugin.mo
> =

> /usr/local/java/lib/locale/zh_TW.BIG5:
> LC_MESSAGES/
> =

> /usr/local/java/lib/locale/zh_TW.BIG5/LC_MESSAGES:
> sunw_java_plugin.mo
> =

> /usr/local/java/lib/security:
> cacerts
> java.policy
> java.security
> =

> /usr/local/java/man:
> ja@
> ja_JP.eucJP/
> man1/
> =

> /usr/local/java/man/ja_JP.eucJP:
> man1/
> =

> /usr/local/java/man/ja_JP.eucJP/man1:
> java.1
> keytool.1
> rmid.1
> rmiregistry.1
> tnameserv.1
> =

> /usr/local/java/man/man1:
> java.1
> keytool.1
> rmid.1
> rmiregistry.1
> tnameserv.1
> =

> /usr/local/java/plugin:
> i386/
> =

> /usr/local/java/plugin/i386:
> ns4/
> ns600/
> =

> /usr/local/java/plugin/i386/ns4:
> javaplugin.so*
> =

> /usr/local/java/plugin/i386/ns600:
> libjavaplugin_oji.so*
> =

> Many thanks for your help,
> =

>   ---------------------------------------------------------------------=
-------------------------------------------------------------------------=
----------------------------------------------------------
>                Name: TEXT.htm
>    TEXT.htm    Type: Hypertext Markup Language (TEXT/HTML)
>            Encoding: base64

-- =

Cheers,
Harry

Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || mangalam@home=
=2Ecom

Re: [GeneX-dev] Re: GeneX listservs and help

[Todd P. <tf...@nc...>]

Don't know the server code hardly at all so it would be ignorant of me to
say how easy or hard it would be. Depends on how much Unix specific stuff is
in the code and how faithfully cygwin reproduces the behavior.

Todd

----- Original Message -----
From: "Harry Mangalam" <hj...@nc...>
To: "Todd Peterson" <tf...@nc...>
Cc: <gen...@li...>; <adl...@uc...>
Sent: Thursday, May 17, 2001 11:04 AM
Subject: [GeneX-dev] Re: GeneX listservs and help


> Well Well well... Then it might mean that we could get GeneX running on
> NT/2k as well?
> Have to think about this, but it might be possible, tho still
> aesthetically ugly... ;)
>
> if apache and cygwin are ok, and you can implement the genex bits on the
> cygwin side (so paths, permissions, system calls etcare handled the
> linux way, then I guess there's no reason that it couldn't work.  R has
> a win port (or probably better to run the Cygwin Linux port)
>
> hjm
>
>
>
>
> Todd Peterson wrote:
> >
> > I have Oracle running on my PC (800 MHz AMD Thunderbird with 512M RAM)
along
> > with Apache. Works fine. Cygwin packages works great, too.
> >
> > ----- Original Message -----
> > From: "Harry Mangalam" <man...@ho...>
> > To: <adl...@uc...>
> > Cc: "genex developers" <gen...@nc...>
> > Sent: Wednesday, May 16, 2001 3:51 PM
> > Subject: GeneX listservs and help
> >
> > > Hi ... sorry I didn't get your 1st name..
> > >
> > > Here are the email addresses to post to if you want help on the genex
> > system:
> > >
> > > ge...@nc... [the NCGR geenx develpers list (~6 developers)]
> > >
> > >
> > > gen...@li... [the larger Open Source group of genex
> > developers ]
> > >
> > > to get the broadest response to your questions, you should post to the
> > genex-dev list.
> > >
> > > We're pretty good at responding to queries right away.
> > >
> > > Hi All,
> > >
> > > Please welcome Thea Wilkins' group from UC Davis.  They have some
> > interesting challenges, like porting to Oracle, running on NT.
> > >
> > > It occurs to me that one thing I DIDN'T consider was that it's
> > theoretically possible (translatation: almost certainly impossible) to
run
> > the GeneX system on a Cygwin-supervised chunk of the system so
> > > that GeneX doesn't know it;s running on NT...?
> > >
> > > Anyone ever tried to run something as complex as a RDBMS on Cygwin?
> > > I know some of my codes which were written explicitly for Unixy OSs
run
> > amazingly well on Cygwin, but it IS another layer to consider and
supporting
> > the bizarrities of Microsoft's OSs is not something
> > > I'm really interested in..
> > >
> > >
> > >
> > > --
> > > Cheers,
> > > Harry
> > >
> > > Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... ||
> > man...@ho...
> > >
>
> --
> Cheers,
> Harry
>
> Harry J Mangalam (949) 856 2847(v&f)  hj...@nc... || man...@ho...
>
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> http://lists.sourceforge.net/lists/listinfo/genex-dev
>

[GeneX-dev] Re: GeneX installation troubleshoot

[Harry M. <hj...@nc...>]

Ron Ophir wrote:
> 
> 
> Dear developers,
> I happened to get to the stage of running install-all.pl. There I had three surprisees: I didn't install xcluster, dtd2html and JAR. For all of these the install-all script (IAS) asked for paths which I couldn't pride. Following that senario I had the following questions and problems:


You have to license xcluster directly from Stanford and compile it
yourself.  Since you are a research org, you can get it for free.


> Assuming I will manage to install these components/applications how do I set their paths. Should I re-run IAS?

Yes.  And you can re-run it with automatic 'Update' mode so that all the
paths should be set automatically.

> I couldn't find dtd2html at the URL specified in the script?

It should be in the same directory as the GeneX-Server:


http://genebox.ncgr.org/download/genex-server/perlSGML.2001Jan23.tar.gz

> Where can I find  a rpm for JAR?

 'jar' is supplied as part of the jdk (Java developer kit) or jre (java
runtime engine) which is available from either 

IBM:
http://alphaworks.ibm.com

or Sun:
http://java.sun.com

I use the IBM one; others use the one from Sun; both work fine, but use
the Java 1.3 package.

> In addition IAS loged out the following error which I presume relate to the fact that dtd2html wasn't installed:


Yes, this is the reason for these errors.  When you install the dtd2html
package, these errors will disappear.  Note that you don't strictly need
the dtd2html for a functional GeneX pkg - only for the generation of the
documentation of the tables.

Please let me know if th


> !! System Error: No such file or directory @ line: 2256  (  -tree  -all genexml-all.html  -dtd genexml  -home genexml-home.html  -out /usr/local/lib/dtd/genexml-html  -top genexml-    top.html  --treefile genexml-tree.html  /usr/local/lib/dtd/genexml.dtd)
> 
> !! System Error: No such file or directory @ line: 2267  (  -tree  -all ams-all.html  -dtd ams  -home ams-home.html  -out /usr/local/lib/dtd/genexml-html  -top ams-top.html  --treefile ams-tree.html  /usr/local/lib/dtd/ams.dtd)
> 
> !! System Error: No such file or directory @ line: 2278  (  -tree  -all als-all.html  -dtd als  -home als-home.html  -out /usr/local/lib/dtd/genexml-html  -top als-top.html  --treefile als-tree.html  /usr/local/lib/dtd/als.dtd)
> 
> !! System Error: No such file or directory @ line: 2289  (  -tree  -all usf-all.html  -dtd usf  -home usf-home.html  -out /usr/local/lib/dtd/genexml-html  -top usf-top.html  --treefile usf-tree.html  /usr/local/lib/dtd/usf.dtd)
> 
> !! System Error: Illegal seek @ line: 2488  (make -s test)
> 
> insn't it?
> 
> Thank you in advance for your support,
> 
> Ron Ophir, Ph.D.
> DNA Microarray Informatics,
> Biological Services
> Weizmann Istitute of Science
> POB 26
> Rehovot 76100
> Israel
> e-mail: Ron...@we...
> Phone: 972-8-9343456
> Fax:972-8-9344113
> 
>   ------------------------------------------------------------------------
> 
>    TEXT.htmName: TEXT.htm
>            Type: Plain Text (text/plain)

-- 
Cheers,
Harry

Harry J Mangalam (949) 856 2847(v&f)  hj...@nc... || man...@ho...