From bizzaro at bc.edu Thu Jul 1 09:40:48 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:41 2006
Subject: [Pipet Devel] workspace shapshot, July 1
Message-ID: <377B6FE0.7D8476E7@bc.edu>
Release early and often, as they say.
Well, I know that most of the people on this list don't have CVS access, so here
is a tarball:
http://theopenlab.um.edu/loci/download/loci-core-19990701.tar.gz
Note that this is what has been on the CVS for about a week, so if you checked
out the module a little while ago (Humberto), there's no need to update.
Requirements:
gnome-libs >= 1.0.10
gnome-python >= 1.0.3
Of course it doesn't do much of anything yet, but I am happy with the look and
feel. Let me know what you think or if you have any ideas.
To get an idea as to what my plans are for the workspace, I have pasted a
message from June 6, "cunstructing the command line":
Locians,
As the development continues, it appears the users will be able to construct
their own gui's by connecting loci together. This will involve the use of an
XML similar to Damon Chaplin's Glade XML, which was really made just to save
projects.
Here is an example of Glade XML. It's simply a button placed in a container and
in a window.
-----------------8<------------------
project1pixmapsCFalseFalsegladesrc.cgladesrc.hgladesig.cgladesig.hGtkWindowwindow1window1GTK_WINDOW_TOPLEVELGTK_WIN_POS_NONETrueTrueFalseGtkFixedfixed1GtkButtonbutton1321611240True
-----------------8<------------------
Note: James Henstridge already made a Python script to generate a PyGTK gui from
Glade XML.
You can see that the widgets here are Gtk widgets; of course, this is for Gtk.
But let's say we make higher level, composite widgets (the "megawidgets" I've
been talking about). Instead simple gui widgets, some of Loci's composite
widgets will generate the options of a command-line. (Some composite widgets
will be biowidgets of a sort.)
For example, in the build phase we start off with a windowlet/locus containing a
composite widget that is an option to choose the name of a program. This may
simply have a text entry box where the user can type in the name.
Next, the user can add a flag option. A new locus appears, and they are
presented with a pull down list of all flags, -a to -Z. Underneath that is a
text entry box that goes with the flag, because sometimes a flag option expects
a term to be added.
And the user can actually specify types and ranges for any option. Say the
program that the gui is being built for requires an integer after the -n flag.
In the build phase, the user can set this using some radio button or something.
At this point the user will see several composite widgets, each with its own
locus, all connected with lines. Selecting the parent locus (the first one
made), the user can pull down a menu and cause them all to be merged into a
functional, gui representation of a command-line. Now that the locus is out of
the build phase, only the options that were not previously set are visible.
I mentioned a couple months ago that there are some programs meant to wrap
command-lines in a gui. GGUI is one that uses wizards:
http://www.greysite.com/ggui/
I also found TkWorld, which is like GGUI:
http://www.tkworld.org/
But Loci is not meant to be just a command-line generator. It will do this, but
much more will be included. For one, Loci will keep biodata in a standardized
XML format. This will require conversion utilities: one for LocusML ->
program-format, and one for program-format -> LocusML. This is because, unlike
simple UNIX shell utilities, most bioinfo programs have specific format
requirements.
Another issue I don't believe is addressed so nicely by GGUI and TkWorld, is
piping. Loci's loci will, by the nature of the bioinfo programs used, make
extensive use of piping or connecting output to input. And this is supposed to
occur seamlessly over the Internet; not something normally done in the UNIX
shell.
So what will the resultant gui XML look like? I think that when the loci are
combined, the XML's can be concatonated. And the user can take them back apart,
recombine them as they wish, and even save/store them. A really neat result is
that a user can make some unique concoction and then send it across the Internet
to someone else using Loci. Rapid locus development and sharing will be
important to Loci's success.
Well, if you read this far, thank you.
:-)
Jeff
--
J.W. Bizzaro mailto:bizzaro@bc.edu
Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/
--
From bizzaro at bc.edu Thu Jul 1 09:44:15 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:42 2006
Subject: [Pipet Devel] the correct address, I think
Message-ID: <377B70AF.AE1B23D1@bc.edu>
uml.edu, not um.edu :-)
http://bioinformatics.org/loci/download/loci-core-19990701.tar.gz
Jeff
--
J.W. Bizzaro mailto:bizzaro@bc.edu
Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/
--
From bizzaro at bc.edu Sun Jul 4 17:08:02 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:42 2006
Subject: [Pipet Devel] Web pages (was: Gary Van Domselaar joins!)
References: <3772F826.4DB9F04B@bc.edu>
Message-ID: <377FCD32.CE2F2D6B@bc.edu>
Gary Van Domselaar wrote:
>
> For my first task I think I should probably flesh out the web site a
> bit. What would you like to see? I personally like the GNOME web page
> design (http://www.gnome.org), which is quite a bit like the loci pages
> are now.
Gary, by "GNOME web page design", do you mean the layout or the graphics? One
of the first Loci (then called TULIP) pages used both the graphics and layout of
GNOME. I have sice changed it quite a bit. The current design looks a little
more like Freshmeat's. I have also tried to keep the Loci pages looking like
other TOL pages.
Can you come up with a one-page prototype so we can get an idea as to how it
would look?
> For starters I propose the following structure:
>
> Main Page - Logo, blurb, and News.
>
> User Info
> Introduction to Loci
> Tour of Loci
> Download
> Documentation
>
> Developer Info
> Introduction (Joining, Background Info & Development Tools)
> Loci Architecture & Systems
> CVS instructions (CVS server?)
> Mailing List
>
> This structure is based loosely on the gnome web pages.
>
Some other things:
User
Screenshots
Developer
List of developers
Development snapshots
We need some CVS instructions for TOL in general. Loci can just have a link to
the TOL page for that.
> I made a couple Loci logos last week when i was playing with the GIMP
> and POVRAY. You can check them out at
> http://redpoll.pharmacy.ualberta.ca/~gvd/loci/
> Give me your input and I will GIMP up an 'official' logo when I get back
Wow! I think they're really nice. I had an idea of my own. I will sketch it
up and post it here soon to see what everyone thinks of it.
>From a recent message:
>
> I hope to have
> the web pages a little more complete by then, so that they can visit the site. I might
> need your help for technical review.
Sure. There are some rather lengthy discussions that we had about Loci's
design. I was thinking that they might be turned into technical essays that we
can post.
> A month isnt a lot of time, so I think I will have
> to do the pages quickly rather than correctly. I'm not super-happy with netscape
> composer, but I think I will develop the pages with it for now.
What have you used before?
> I'd like the option of
> writing php for dynamic web page generation, but I dont think it is activated in the
> apache web server right now.
Hmmm. Alan Williams (Alan@TheWilliamsFamily.org) just offered to do some PHP
scripting too. Maybe you too can work together on this? One thing we were
looking to do was put a table of contents on the right side of each Loci page.
But it would have to be dynamically generated in case there are some changes. I
started doing this statically, but it just became too much to keep up with as I
added new pages.
:-)
Jeff
--
J.W. Bizzaro mailto:bizzaro@bc.edu
Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/
--
From gvd at redpoll.pharmacy.ualberta.ca Sun Jul 4 21:54:50 1999
From: gvd at redpoll.pharmacy.ualberta.ca (Gary Van Domselaar)
Date: Fri Feb 10 19:18:42 2006
Subject: [Pipet Devel] Web pages
In-Reply-To: <199907050018.SAA00608@gvd.v-wave.com>
Message-ID:
On Sun, 4 Jul 1999, Gary Van Domselaar wrote:
> Gary, by "GNOME web page design", do you mean the layout or the graphics?
Both.
>
> Can you come up with a one-page prototype so we can get an idea as to how it
> would look?
no prob.
> Some other things:
User
Screenshots
Developer
List of developers
Development snapshots
Got it.
I'd like the option of
> > writing php for dynamic web page generation, but I dont think it is activated in the
> > apache web server right now.
>
> Hmmm. Alan Williams (Alan@TheWilliamsFamily.org) just offered to do some PHP
> scripting too. Maybe you too can work together on this? One thing we were
> looking to do was put a table of contents on the right side of each Loci page.
> But it would have to be dynamically generated in case there are some changes. I
> started doing this statically, but it just became too much to keep up with as I
> added new pages.
>
Let me see what I can do with php. Website Meta Language (WML)
(http://www.engelschall.com/sw/wml/) may also be useful here.
> From a recent message:
> >
> > I hope to have
> > the web pages a little more complete by then, so that they can visit the site. I might
> > need your help for technical review.
>
> Sure. There are some rather lengthy discussions that we had about Loci's
> design. I was thinking that they might be turned into technical essays that we
> can post.
Thats what I was thinking as well.
>
> > A month isnt a lot of time, so I think I will have
> > to do the pages quickly rather than correctly. I'm not super-happy with netscape
> > composer, but I think I will develop the pages with it for now.
>
> What have you used before?
Composer, vi, and perl. The problem with composer is the way it gets
confused about nested bullets and list items, and the way it reformats
the html.
A friend of mine suggested I use cascading style sheets to format the web
pages, which is more line with the XML concept than standard html. I'll
check out some tutorials on it and then decide if i can tackle the loci
pages that way. Would I be correct to assume that the html generation
technology that we adopt will be used for TOL pages as well?
--Gary
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Gary Van Domselaar gvd@redpoll.pharmacy.ualberta.ca
Faculty of Pharmacy Phone: (780) 492-4493
University of Alberta FAX: (780) 492-5305
Edmonton, Alberta, Canada
From stein at fmppr.fmnh.org Wed Jul 7 17:38:36 1999
From: stein at fmppr.fmnh.org (J. Steinbachs)
Date: Fri Feb 10 19:18:42 2006
Subject: [Pipet Devel] bioinformatics online info
References:
Message-ID: <3783C8DC.958469C7@fmnh.org>
Just thought I'd share my latest bioinformatics web finds (my Museum
curator colleagues really don't care about this stuff):
http://www.bioinfo.de/isb/
In their set of inaugural articles, take a peek at SEView, a java applet
for viewing molecular sequence data.
http://www.bitsjournal.com/bits.html
Some interesting reading (more likely for the powers-that-be) on the
merging of IT and biology (and voila, we have bioinformatics). A useful
(albeit somewhat biased) article out of Oracle on CORBA and its
applications to bioinformatics projects.
--------------------------
Jennifer Steinbachs
Computational Biologist
Dept. of Botany
The Field Museum
Chicago, IL 60605-2496
office: 312-665-7810
fax: 312-665-7158
--------------------------
From bizzaro at bc.edu Wed Jul 7 23:49:43 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:42 2006
Subject: [Pipet Devel] bioinformatics online info
References: <3783C8DC.958469C7@fmnh.org>
Message-ID: <37841FD7.1411C2D9@bc.edu>
Eeek. New journals are popping up everywhere! So how many are there now?
Bioinformatics (CABIOS)
Journal of Computational Biology
Gene COMBIS
ISB
BITS
Any others? How about
BioInfo
:-)
Jeff
"J. Steinbachs" wrote:
>
> Just thought I'd share my latest bioinformatics web finds (my Museum
> curator colleagues really don't care about this stuff):
>
> http://www.bioinfo.de/isb/
> In their set of inaugural articles, take a peek at SEView, a java applet
> for viewing molecular sequence data.
>
> http://www.bitsjournal.com/bits.html
> Some interesting reading (more likely for the powers-that-be) on the
> merging of IT and biology (and voila, we have bioinformatics). A useful
> (albeit somewhat biased) article out of Oracle on CORBA and its
> applications to bioinformatics projects.
>
> --------------------------
> Jennifer Steinbachs
> Computational Biologist
> Dept. of Botany
> The Field Museum
> Chicago, IL 60605-2496
>
> office: 312-665-7810
> fax: 312-665-7158
> --------------------------
>
> _______________________________________________
> pipet-devel maillist - pipet-devel@bioinformatics.org
> http://bioinformatics.org/mailman/listinfo/pipet-devel
--
J.W. Bizzaro mailto:bizzaro@bc.edu
Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/
--
From bizzaro at bc.edu Wed Jul 7 23:56:21 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:42 2006
Subject: [Pipet Devel] bioinformatics online info
References: <3783C8DC.958469C7@fmnh.org>
Message-ID: <37842165.C2C38A00@bc.edu>
"J. Steinbachs" wrote:
>
> http://www.bioinfo.de/isb/
> In their set of inaugural articles, take a peek at SEView, a java applet
> for viewing molecular sequence data.
Wow! Hey this is exactly what we're looking for some of the translators to do!
This is required reading :-) Here is a direct link:
http://www.bioinfo.de/isb/1998/01/0003/
Jeff
--
J.W. Bizzaro mailto:bizzaro@bc.edu
Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/
--
From pmr at sanger.ac.uk Thu Jul 8 04:06:39 1999
From: pmr at sanger.ac.uk (Peter Rice)
Date: Fri Feb 10 19:18:42 2006
Subject: [Pipet Devel] bioinformatics online info
In-Reply-To: <37841FD7.1411C2D9@bc.edu> (bizzaro@bc.edu)
References: <3783C8DC.958469C7@fmnh.org> <37841FD7.1411C2D9@bc.edu>
Message-ID: <199907080806.JAA12870@europa.sanger.ac.uk>
Jeff Bizarro writes:
>Eeek. New journals are popping up everywhere! So how many are there now?
EMBnet.News
http://www.uk.embnet.org/embnet.news/
BioInformer (from EBI)
http://bioinformer.ebi.ac.uk/
BioInform
http://www.bioinform.com/
UK CCP11 Newsletter
http://www.hgmp.mrc.ac.uk/CCP11/newsletter/
Genome Research also publishes genome bioinformatics articles
--
----------------------------------------------------------------------
Peter Rice | Informatics Division, The Sanger Centre,
E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus,
Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England
Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/
From David.Lapointe at umassmed.edu Thu Jul 8 11:00:07 1999
From: David.Lapointe at umassmed.edu (Lapointe, David)
Date: Fri Feb 10 19:18:42 2006
Subject: [Pipet Devel] bioinformatics online info
Message-ID: <93307F07DE63D211B2F30000F808E9E501644D05@edunivexch02.umassmed.edu>
How about
Genome Research
Protein Science [?]
David Lapointe
Manager - Research Computing Services
UMass Medical School
Worcester, MA 01655
508/856-5141
> -----Original Message-----
> From: J.W. Bizzaro [mailto:bizzaro@bc.edu]
> Sent: Wednesday, July 07, 1999 11:50 PM
> To: pipet-devel@bioinformatics.org
> Subject: Re: [Pipet Devel] bioinformatics online info
>
>
> Eeek. New journals are popping up everywhere! So how many
> are there now?
>
> Bioinformatics (CABIOS)
> Journal of Computational Biology
> Gene COMBIS
> ISB
> BITS
>
> Any others? How about
>
> BioInfo
>
> :-)
> Jeff
>
>
> "J. Steinbachs" wrote:
> >
> > Just thought I'd share my latest bioinformatics web finds (my Museum
> > curator colleagues really don't care about this stuff):
> >
> > http://www.bioinfo.de/isb/
> > In their set of inaugural articles, take a peek at SEView,
> a java applet
> > for viewing molecular sequence data.
> >
> > http://www.bitsjournal.com/bits.html
> > Some interesting reading (more likely for the powers-that-be) on the
> > merging of IT and biology (and voila, we have
> bioinformatics). A useful
> > (albeit somewhat biased) article out of Oracle on CORBA and its
> > applications to bioinformatics projects.
> >
> > --------------------------
> > Jennifer Steinbachs
> > Computational Biologist
> > Dept. of Botany
> > The Field Museum
> > Chicago, IL 60605-2496
> >
> > office: 312-665-7810
> > fax: 312-665-7158
> > --------------------------
> >
> > _______________________________________________
> > pipet-devel maillist - pipet-devel@bioinformatics.org
> > http://bioinformatics.org/mailman/listinfo/pipet-devel
>
> --
> J.W. Bizzaro mailto:bizzaro@bc.edu
> Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/
> --
>
> _______________________________________________
> pipet-devel maillist - pipet-devel@bioinformatics.org
> http://bioinformatics.org/mailman/listinfo/pipet-devel
>
From stein at fmppr.fmnh.org Thu Jul 8 11:19:44 1999
From: stein at fmppr.fmnh.org (J. Steinbachs)
Date: Fri Feb 10 19:18:42 2006
Subject: [Pipet Devel] bioinformatics online info
References: <3783C8DC.958469C7@fmnh.org> <37841FD7.1411C2D9@bc.edu>
Message-ID: <3784C190.3C78994D@fmnh.org>
"J.W. Bizzaro" wrote:
>
> Eeek. New journals are popping up everywhere! So how many are there now?
>
> Bioinformatics (CABIOS)
> Journal of Computational Biology
> Gene COMBIS
Sadly, if you go to Elsevier's site and read the little scrolly banner
in the bottom (in Netscape), you will notice that Gene-COMBIS has been
discontinued as of this year.
I'm putting together a set of bookmarks for online computational biology
related journals. When I get them together (and get a machine set up),
I'll point you to the URL.
--------------------------
Jennifer Steinbachs
Computational Biologist
Dept. of Botany
The Field Museum
Chicago, IL 60605-2496
office: 312-665-7810
fax: 312-665-7158
--------------------------
From bizzaro at bc.edu Fri Jul 9 01:48:35 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:42 2006
Subject: [Pipet Devel] freshmeat announcement
Message-ID: <37858D33.4AFB0D3B@bc.edu>
I just made the first announcement about Loci at freshmeat.net. I know we don't
have much to show, but I intended this to be a general announcement about the
project. In the future, we can just post "loci-core X.X.X", "loci-daemon
X.X.X", etc. In just over an hour, the page got hit as much as it does in a
whole day :-) Here is what I posted:
The Loci Project (alpha)
J.W. Bizzaro - July 08th 1999, 23:05 EST
Loci is a network-distributed system of clients and servers ("loci") for
computational biology research. The loci are data, high-level widgets,
analysis
programs (command-line), data translators, vector drawing programs, and any
combination of these. They are represented as nodes on a graphical "work flow
diagram" (WFD) and can be connected in a manner akin to Unix piping. In a
sense,
Loci is a graphical scripting language where users can build, customize and
execute
their own scriptlets via the WFD. Plus, connecting loci across the Internet,
can form
world-wide collaboratives and an infinitely extensible set of loci. Numerous
development tools used include Python, GTK+ and the GNOME environment:
CORBA, DOM, XML and so on. Although Loci is being developed for computational
biology (for which it is highly suited), the system's core is not dependent
on a
particular data type. THIS IS ALPHA SOFTWARE!
Jeff
--
J.W. Bizzaro mailto:bizzaro@bc.edu
Boston College Chemistry http://www.uml.edu/Dept/Chem/Bizzaro/
--
From bizzaro at bc.edu Fri Jul 9 16:31:17 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:42 2006
Subject: [Pipet Devel] [Fwd: Meta-Application Interface: a proposal]
Message-ID: <37865C15.F2CF764F@bc.edu>
Locians,
Ferdinando Villa posted this message to one of the Gnome mailing lists. His
idea reminded me so much of Loci that I contacted him. I will forward the rest
of our correspondence next. Jeff
-------------- next part --------------
An embedded message was scrubbed...
From: Ferdinando Villa
Subject: Meta-Application Interface: a proposal
Date: Thu, 17 Jun 1999 14:42:39 -0400 (EDT)
Size: 7004
Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990709/55724ed1/attachment.mht
From bizzaro at bc.edu Fri Jul 9 16:32:25 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:42 2006
Subject: [Pipet Devel] [Fwd: Meta-Application Interface: a proposal]
Message-ID: <37865C59.F99A9594@bc.edu>
I guess I did send this message to the list before. But here it is again.
-------------- next part --------------
An embedded message was scrubbed...
From: "J.W. Bizzaro"
Subject: Re: Meta-Application Interface: a proposal
Date: Fri, 18 Jun 1999 00:19:07 +0000
Size: 8791
Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990709/5dd02d9a/attachment.mht
From bizzaro at bc.edu Fri Jul 9 16:32:51 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:42 2006
Subject: [Pipet Devel] [Fwd: Meta-Application Interface: a proposal]
Message-ID: <37865C73.2E131A88@bc.edu>
-------------- next part --------------
An embedded message was scrubbed...
From: Ferdinando Villa
Subject: Re: Meta-Application Interface: a proposal
Date: Fri, 9 Jul 1999 10:12:02 -0400 (EDT)
Size: 6196
Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990709/2bfb8509/attachment.mht
From bizzaro at bc.edu Fri Jul 9 16:33:37 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:43 2006
Subject: [Pipet Devel] [Fwd: Meta-Application Interface: a proposal]
Message-ID: <37865CA1.F91D955@bc.edu>
-------------- next part --------------
An embedded message was scrubbed...
From: "J.W. Bizzaro"
Subject: Re: Meta-Application Interface: a proposal
Date: Fri, 09 Jul 1999 19:48:10 +0000
Size: 6813
Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990709/85d94a02/attachment.mht
From bizzaro at bc.edu Fri Jul 9 16:34:47 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:43 2006
Subject: [Pipet Devel] [Fwd: Meta-Application Interface: a proposal]
Message-ID: <37865CE7.10662C54@bc.edu>
I hope to continue this conversation on this list.
-------------- next part --------------
An embedded message was scrubbed...
From: Ferdinando Villa
Subject: Re: Meta-Application Interface: a proposal
Date: Fri, 9 Jul 1999 16:08:26 -0400 (EDT)
Size: 5214
Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990709/fa082f4f/attachment.mht
From bizzaro at bc.edu Fri Jul 9 18:35:32 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:43 2006
Subject: [Pipet Devel] loci-core-19990708
Message-ID: <37867934.DEA4E9B0@bc.edu>
Here is a new snapshot:
http://bioinformatics.org/loci/download/loci-core-19990708.tar.gz
For those new to the list, remember that all you can do is move some pretty
little boxes around. This is NOT a functional application yet.
You need:
gnome-libs 1.0.10
gnome-python 1.0.3
And of course what those need.
I got scrollbars for the workspace now. The next thing I'll be working on is
getting the workspace/canvas to grow in size when an object pushes beyond the
boundaries. Any ideas? I think if I can get the bounds of all objects, I can
check them against the bounds when they are moved (or maybe just dropped) and
then resize the workspace if needed.
:-)
Jeff
--
+------------------------------------+
| |
| J.W. Bizzaro |
| jeff@bioinformatics.org |
| |
| THE OPEN COLLABORATORY |
| FOR MOLECULAR BIOINFORMATICS |
| |
| http://bioinformatics.org/ |
| |
+------------------------------------+
From justin at ukans.edu Fri Jul 9 23:37:24 1999
From: justin at ukans.edu (Justin Bradford)
Date: Fri Feb 10 19:18:43 2006
Subject: [Pipet Devel] DOM/gdome update
Message-ID:
I've contacted the author of gdome, and am actively tracking its
development. Unfortunately, little is being done with it currently. Most
of its development is being driven by gill (an SVG application).
Anyway, I've talked to the primary author of gdome. His plans for the
sliding DOM have been set aside, and they are currently concentrated on
implementing a straight DOM interface over CORBA. He was very interested
in my ideas on a simple wire protocol (something that would not require
CORBA, necessarily), and I'll be getting back to him with a proposal for
an intelligent client-side gdome interface (which resolves many of the
problems with DOM over CORBA).
However, the first priority for this side of development is probably
python bindings to CORBA. I'll be checking into that this weekend. With
the new design, supposedly new language bindings are not too difficult.
Hopefully, I can get something working soon which will allow use of
GNOME's CORBA stuff. We can use the convential gdome system for the
interim, and eventually, the new, more efficient (but not quite
traditional DOM) interface will be available for implementing our various
tools.
Is everyone ok with the idea of a centralized gdome system holding the
Loci data? Plugins (viewers, editors, etc) all deal with the data via the
gdome interface. It offers some very cool benefits with little (Loci
unique) code, so as event notification, locking, etc.
I've been busy at Genentech lately, but I just wrapped up a project, so I
can hopefully do something for Loci now, besides write emails about what
I'm going to do ;)
And for anyone who cares, Genentech (the original biotech company, based
in San Francisco) is a very cool place. And it looks like they're going to
give me a job next January, and probably pay for grad school. The
bioinformatics/biocomputing departments are expanding rapidly for anyone
looking for jobs :)
Justin
From bizzaro at bc.edu Sat Jul 10 01:17:13 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:43 2006
Subject: [Pipet Devel] DOM/gdome update
References:
Message-ID: <3786D759.2B5260FC@bc.edu>
Justin Bradford wrote:
>
> I've contacted the author of gdome, and am actively tracking its
> development. Unfortunately, little is being done with it currently. Most
> of its development is being driven by gill (an SVG application).
Hi Justin. Who's the author of gdome?
> Anyway, I've talked to the primary author of gdome. His plans for the
> sliding DOM have been set aside, and they are currently concentrated on
> implementing a straight DOM interface over CORBA. He was very interested
> in my ideas on a simple wire protocol (something that would not require
> CORBA, necessarily), and I'll be getting back to him with a proposal for
> an intelligent client-side gdome interface (which resolves many of the
> problems with DOM over CORBA).
Hmmm. I don't recall if you mentioned a "wire protocol" before on this list.
Feel free to share the proposal with us when it's ready.
> However, the first priority for this side of development is probably
> python bindings to CORBA. I'll be checking into that this weekend. With
> the new design, supposedly new language bindings are not too difficult.
Great. Did you post on the ORBit list that you'll be working on the bindings?
The Python newsgroup might be a good place to announce that too.
> Hopefully, I can get something working soon which will allow use of
> GNOME's CORBA stuff. We can use the convential gdome system for the
> interim, and eventually, the new, more efficient (but not quite
> traditional DOM) interface will be available for implementing our various
> tools.
Neeto. But I think most of us will need a primer on using CORBA and DOM. Is
there some documentation that you think would be helpful?
> Is everyone ok with the idea of a centralized gdome system holding the
> Loci data? Plugins (viewers, editors, etc) all deal with the data via the
> gdome interface. It offers some very cool benefits with little (Loci
> unique) code, so as event notification, locking, etc.
The last messages I posted from Ferdinando pointed out that there are quite a
few guys around with somewhat similar plans for Gnome. If we all work together,
we will have something that much better and sooner. And I think if we decide to
use Gnome, we should get more than just our feet wet and try to work on some
Gnome development (blur the line between Gnome and Loci). This way we will
understand the system better and get to know (and maybe get some help from) the
Gnome developers. Some of those guys (and some of you guys :-) are way ahead of
me, and I'd love to work with them.
> I've been busy at Genentech lately, but I just wrapped up a project, so I
> can hopefully do something for Loci now, besides write emails about what
> I'm going to do ;)
:-)
> And for anyone who cares, Genentech (the original biotech company, based
> in San Francisco) is a very cool place. And it looks like they're going to
> give me a job next January, and probably pay for grad school. The
> bioinformatics/biocomputing departments are expanding rapidly for anyone
> looking for jobs :)
Congratulations!
Cheers.
Jeff
P.S. We got 301 hits on the Loci page Friday, due mostly to the Freshmeat post.
And there are 2 new subscribers to the list.
--
+------------------------------------+
| |
| J.W. Bizzaro |
| jeff@bioinformatics.org |
| |
| THE OPEN COLLABORATORY |
| FOR MOLECULAR BIOINFORMATICS |
| |
| http://bioinformatics.org/ |
| |
+------------------------------------+
From hortiz at neurobio.upr.clu.edu Mon Jul 12 11:17:59 1999
From: hortiz at neurobio.upr.clu.edu (Humberto Ortiz Zuazaga)
Date: Fri Feb 10 19:18:43 2006
Subject: [Pipet Devel] DOM/gdome update
In-Reply-To: Your message of "Fri, 09 Jul 1999 22:37:24 EST."
Message-ID: <199907121518.LAA18473@chimbo.neurobio.upr.clu.edu>
> Is everyone ok with the idea of a centralized gdome system holding the
> Loci data? Plugins (viewers, editors, etc) all deal with the data via the
> gdome interface. It offers some very cool benefits with little (Loci
> unique) code, so as event notification, locking, etc.
This sounds great, especially if you can keep the API the same over corba or
the light weight transport.
--
Humberto Ortiz Zuazaga
Bioinformatics Specialist
Institute of Neurobiology
hortiz@neurobio.upr.clu.edu
From bizzaro at bc.edu Mon Jul 12 21:35:45 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:43 2006
Subject: [Pipet Devel] gnome-filer (fwd)
Message-ID: <378A97F1.BD3F6D91@bc.edu>
Here is a message from David Orme to Ferdinando Villa about gnome-filer. Recall
that Ferdinando said he would send us this message. Jeff
-------------- next part --------------
An embedded message was scrubbed...
From: Ferdinando Villa
Subject: Re: Meta-Application Interface: a proposal (fwd)
Date: Mon, 12 Jul 1999 11:42:36 -0400 (EDT)
Size: 1245
Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990713/1f795057/attachment.mht
From bizzaro at bc.edu Mon Jul 12 22:37:59 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:43 2006
Subject: [Pipet Devel] [Fwd: The Loci Project]
Message-ID: <378AA687.E6C33B47@bc.edu>
Here is a reply from Thomas Junier, co-author of SEView. Recall that Jennifer
sent us a link to his article in ISB:
http://www.bioinfo.de/isb/1998/01/0003/
I sent a message to Thomas and the other author, Philipp, to see if they would
like to help with Loci. Jeff
-------------- next part --------------
An embedded message was scrubbed...
From: Thomas Junier
Subject: Re: The Loci Project
Date: Sun, 11 Jul 1999 10:11:32 +0200
Size: 4240
Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990713/38c33b1d/attachment.mht
From bizzaro at bc.edu Tue Jul 13 00:13:34 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:44 2006
Subject: [Pipet Devel] Web server is down for upgrading
Message-ID: <378ABCEE.BCBD6C7B@bc.edu>
Greetings.
We're sorry to say that Web access to The Open Lab will be unavailable for a
short while. We are trying to upgrade some of the software. However, other
services like SSH are still up.
I will send another message when the Web server is operational.
Cheers.
Jeff
--
+------------------------------------+
| |
| J.W. Bizzaro |
| jeff@bioinformatics.org |
| |
| THE OPEN COLLABORATORY |
| FOR MOLECULAR BIOINFORMATICS |
| |
| http://bioinformatics.org/ |
| |
+------------------------------------+
From bizzaro at bc.edu Tue Jul 13 18:35:51 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:44 2006
Subject: [Pipet Devel] Web server is back up
Message-ID: <378BBF47.F5B370B8@bc.edu>
Hello again.
We ran into some configuration problems. The server is back up and running, but
PHP support is still in the queue, so to speek.
:-)
Jeff
--
+------------------------------------+
| |
| J.W. Bizzaro |
| jeff@bioinformatics.org |
| |
| THE OPEN COLLABORATORY |
| FOR MOLECULAR BIOINFORMATICS |
| |
| http://bioinformatics.org/ |
| |
+------------------------------------+
From stein at fmppr.fmnh.org Wed Jul 14 10:56:01 1999
From: stein at fmppr.fmnh.org (J. Steinbachs)
Date: Fri Feb 10 19:18:44 2006
Subject: [Pipet Devel] Another (java) bioinformatics tool
Message-ID: <378CA501.BF684F80@fmnh.org>
To all:
I stumbled across this reference last night. Anybody know anything
about it? (free? commercial? good? bad?) Sadly, I don't have access
to this journal either in paper format (except through interlibrary
loan) or online...
Gregg A. Helt, Suzanna Lewis, Ann E. Loraine, and Gerald M. Rubin
BioViews: Java-Based Tools for Genomic Data Visualization
Genome Res. 1998 8: 291-305. [Abstract] [Full Text]
-jennifer
--------------------------
Jennifer Steinbachs
Computational Biologist
Dept. of Botany
The Field Museum
Chicago, IL 60605-2496
office: 312-665-7810
fax: 312-665-7158
--------------------------
From hortiz at neurobio.upr.clu.edu Wed Jul 14 11:33:50 1999
From: hortiz at neurobio.upr.clu.edu (Humberto Ortiz Zuazaga)
Date: Fri Feb 10 19:18:44 2006
Subject: [Pipet Devel] Another (java) bioinformatics tool
In-Reply-To: Your message of "Wed, 14 Jul 1999 09:56:01 EST."
<378CA501.BF684F80@fmnh.org>
Message-ID: <199907141533.LAA01385@chimbo.neurobio.upr.clu.edu>
> I stumbled across this reference last night. Anybody know anything
> about it?
>
> Gregg A. Helt, Suzanna Lewis, Ann E. Loraine, and Gerald M. Rubin
> BioViews: Java-Based Tools for Genomic Data Visualization
> Genome Res. 1998 8: 291-305. [Abstract] [Full Text]
Try:
http://www.fruitfly.org/bioviews/
I thought this project had been merged with the BioWidgets for Java project,
but this web page looks pretty active. You can find some more links off my
computational molecular biology page:
http://www.neurobio.upr.clu.edu/~hortiz/cmb/
--
Humberto Ortiz Zuazaga
Bioinformatics Specialist
Institute of Neurobiology
hortiz@neurobio.upr.clu.edu
From hortiz at neurobio.upr.clu.edu Wed Jul 14 11:37:20 1999
From: hortiz at neurobio.upr.clu.edu (Humberto Ortiz Zuazaga)
Date: Fri Feb 10 19:18:44 2006
Subject: [Pipet Devel] Another (java) bioinformatics tool
In-Reply-To: Your message of "Wed, 14 Jul 1999 09:56:01 EST."
<378CA501.BF684F80@fmnh.org>
Message-ID: <199907141537.LAA01415@chimbo.neurobio.upr.clu.edu>
> BioViews: Java-Based Tools for Genomic Data Visualization
Sorry, damn frames, the correct url is:
http://www.fruitfly.org/displays/
--
Humberto Ortiz Zuazaga
Bioinformatics Specialist
Institute of Neurobiology
hortiz@neurobio.upr.clu.edu
From gvd at redpoll.pharmacy.ualberta.ca Thu Jul 15 02:35:14 1999
From: gvd at redpoll.pharmacy.ualberta.ca (Gary Van Domselaar)
Date: Fri Feb 10 19:18:44 2006
Subject: [Pipet Devel] PHP is up
In-Reply-To: <378BBF47.F5B370B8@bc.edu> from "J.W. Bizzaro" at Jul 13, 99 10:35:51 pm
Message-ID: <199907150635.AAA25474@redpoll.pharmacy.ualberta.ca>
Locians,
PHP is now running on the apache server. Some of you may know that PHP is
a server-parsed web-scripting language that allows you to make
sophisticated dynamic HTML pages easily. I've also allowed read-only
access to user directories for those of you who are interested in doing
some php development. I'll use it primarily to index the website, but its
useful for other things too. One of PHP's strongest features is database
integration (excite uses PHP). I was thinking it might be nice some day
to use PHP to create a "bioinformatics portal" as a resource to the
community.
I'll get to work on some template pages for loci hopefully sometime next
week.
--Gary
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Gary Van Domselaar gvd@redpoll.pharmacy.ualberta.ca
Faculty of Pharmacy Phone: (780) 492-4493
University of Alberta FAX: (780) 492-5305
Edmonton, Alberta, Canada
From justin at ukans.edu Thu Jul 15 05:29:33 1999
From: justin at ukans.edu (Justin Bradford)
Date: Fri Feb 10 19:18:44 2006
Subject: [Pipet Devel] PHP is up
In-Reply-To: <199907150635.AAA25474@redpoll.pharmacy.ualberta.ca>
Message-ID:
> I was thinking it might be nice some day
> to use PHP to create a "bioinformatics portal" as a resource to the
> community.
Ok, but I get in on the IPO, right? ;)
Oh, has anyone here seem Spotfire's analysis software? I caught a demo
today, and some of the UI stuff was pretty interesting. It was basically
just a graphing engine, but it you could really tweak the display and go
through a lot of data visually, very quickly.
Justin
From David.Lapointe at umassmed.edu Thu Jul 15 11:46:34 1999
From: David.Lapointe at umassmed.edu (Lapointe, David)
Date: Fri Feb 10 19:18:44 2006
Subject: [Pipet Devel] PHP is up
Message-ID: <93307F07DE63D211B2F30000F808E9E501644D19@edunivexch02.umassmed.edu>
Yes, I saw an article and a review in the HMSBeagle this week. It reminded
me of some AVS applications for SciVi that I have seen in the past.
Basically dealing with the problem of multidimensional data visualization.
The review of Spotfire seemed a little less than glowing.
David Lapointe
Manager - Research Computing Services
UMass Medical School
Worcester, MA 01655
508/856-5141
> -----Original Message-----
> From: Justin Bradford [mailto:justin@ukans.edu]
> Sent: Thursday, July 15, 1999 5:30 AM
> To: pipet-devel@bioinformatics.org
> Subject: Re: [Pipet Devel] PHP is up
>
>
> > I was thinking it might be nice some day
> > to use PHP to create a "bioinformatics portal" as a resource to the
> > community.
>
> Ok, but I get in on the IPO, right? ;)
>
> Oh, has anyone here seem Spotfire's analysis software? I caught a demo
> today, and some of the UI stuff was pretty interesting. It
> was basically
> just a graphing engine, but it you could really tweak the
> display and go
> through a lot of data visually, very quickly.
>
> Justin
>
>
> _______________________________________________
> pipet-devel maillist - pipet-devel@bioinformatics.org
> http://bioinformatics.org/mailman/listinfo/pipet-devel
>
From bizzaro at bc.edu Thu Jul 15 23:14:10 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:44 2006
Subject: [Pipet Devel] PHP is up
References: <199907150635.AAA25474@redpoll.pharmacy.ualberta.ca>
Message-ID: <378EA382.98F11F34@bc.edu>
Gary Van Domselaar wrote:
> I was thinking it might be nice some day
> to use PHP to create a "bioinformatics portal" as a resource to the
> community.
That may be what BioInfo is in some ways:
http://bioinformatics.org/bioinfo/
What do you think should be in a bioinformatics portal?
:-)
Jeff
--
+------------------------------------+
| |
| J.W. Bizzaro |
| jeff@bioinformatics.org |
| |
| THE OPEN COLLABORATORY |
| FOR MOLECULAR BIOINFORMATICS |
| |
| http://bioinformatics.org/ |
| |
+------------------------------------+
From bizzaro at bc.edu Thu Jul 15 23:45:01 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:44 2006
Subject: [Pipet Devel] XML Script
Message-ID: <378EAABD.D156864C@bc.edu>
Interesting:
http://www.xmlscript.org/
I wonder how this would merge with the Workflow Diagram's "graphical command
language".
Jeff
--
+------------------------------------+
| |
| J.W. Bizzaro |
| jeff@bioinformatics.org |
| |
| THE OPEN COLLABORATORY |
| FOR MOLECULAR BIOINFORMATICS |
| |
| http://bioinformatics.org/ |
| |
+------------------------------------+
From stein at fmppr.fmnh.org Fri Jul 16 13:32:52 1999
From: stein at fmppr.fmnh.org (J. Steinbachs)
Date: Fri Feb 10 19:18:45 2006
Subject: [Pipet Devel] UMN's CompBio resources
References: <199907141537.LAA01415@chimbo.neurobio.upr.clu.edu>
Message-ID: <378F6CC4.14E12147@fmnh.org>
More online resources...
U. Minnesota's Computational Biology Center: http://www.cbc.umn.edu/
In their "research projects -> papers" links, check out
http://www.cbc.umn.edu/VirtLibrary/Shoop/SAC93/SAC93.paper.ss.html
--------------------------
Jennifer Steinbachs
Computational Biologist
Dept. of Botany
The Field Museum
Chicago, IL 60605-2496
office: 312-665-7810
fax: 312-665-7158
email: stein@fmnh.org
--------------------------
From bizzaro at bc.edu Mon Jul 19 01:20:02 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:45 2006
Subject: [Pipet Devel] gamora
Message-ID: <3792B582.85FECAE6@bc.edu>
Some similarities to Loci:
http://gamora.org/
A little hard to grasp. It's not a bioinformatics app.
Jeff
--
+------------------------------------+
| |
| J.W. Bizzaro |
| jeff@bioinformatics.org |
| |
| THE OPEN COLLABORATORY |
| FOR MOLECULAR BIOINFORMATICS |
| |
| http://bioinformatics.org/ |
| |
+------------------------------------+
From gvd at redpoll.pharmacy.ualberta.ca Mon Jul 19 01:43:31 1999
From: gvd at redpoll.pharmacy.ualberta.ca (Gary Van Domselaar)
Date: Fri Feb 10 19:18:45 2006
Subject: [Pipet Devel] PHP is up
References: <199907150635.AAA25474@redpoll.pharmacy.ualberta.ca> <378EA382.98F11F34@bc.edu>
Message-ID: <3792BB03.64E45411@redpoll.pharmacy.ualberta.ca>
J.W. Bizzaro wrote:
>
> That may be what BioInfo is in some ways:
>
> http://bioinformatics.org/bioinfo/
>
> What do you think should be in a bioinformatics portal?
>
TOL's bioinfo is _exactly_ what I was thinking ;-) Add hot current
events in bioinformatics with a hierachically organized database like
yahoo. Then we pass an XML standard for bioinformatics documents that
allows us to catalog them in our database. Once XML takes over the
Internet we release a web-crawler that updates the database
automagically. Then we sit back and get rich and fat.
--Gary
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Gary Van Domselaar gvd@redpoll.pharmacy.ualberta.ca
Faculty of Pharmacy Phone: (780) 492-4493
University of Alberta FAX: (780) 492-5305
Edmonton, Alberta, Canada http://redpoll.pharmacy.ualberta.ca/~gvd
From bizzaro at bc.edu Mon Jul 19 06:58:51 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:45 2006
Subject: [Pipet Devel] GtkGLArea gets Python wrapper
Message-ID: <379304EB.8EAA2327@bc.edu>
Locians,
Very good news:
James Henstridge writes:
> In other news, I have added a wrapper for gtkglarea to pygtk. There are a
> few examples in the examples/gl directory, including a translation of the
> mesa gears demo. To use it, you will also need the PyOpenGL package.
GtkGLArea is the Gtk drawing area/widget for OpenGL:
http://www.student.oulu.fi/~jlof/gtkglarea/
I wrote to James about making a Python wrapper for it, and well, he just did.
The bottom line for us is that we can make Python-based widgets for Loci to
render 3D models. Very cool. This brings us another step closer to integrating
AMMP and MMTk.
Cheers.
Jeff
--
+------------------------------------+
| |
| J.W. Bizzaro |
| jeff@bioinformatics.org |
| |
| THE OPEN COLLABORATORY |
| FOR MOLECULAR BIOINFORMATICS |
| |
| http://bioinformatics.org/ |
| |
+------------------------------------+
From Alan at TheWilliamsFamily.org Mon Jul 19 10:23:38 1999
From: Alan at TheWilliamsFamily.org (Alan J. Williams)
Date: Fri Feb 10 19:18:45 2006
Subject: [Pipet Devel] PHP is up
In-Reply-To: <3792BB03.64E45411@redpoll.pharmacy.ualberta.ca>
Message-ID:
Along these lines, I have started to put together a bioinformatics and
molecular biology jump site at www.molbio.org. Currently the only thing
up and running is the news service. It allows for posting to molbio.org
by anyone from the web. I want to add a catalog of web resources that can
be updated by anyone from the web before I announce the site, which is why
I haven't mentioned it to date.
On Sun, 18 Jul 1999, Gary Van Domselaar wrote:
> > What do you think should be in a bioinformatics portal?
>
> TOL's bioinfo is _exactly_ what I was thinking ;-) Add hot current
> events in bioinformatics with a hierachically organized database like
> yahoo. Then we pass an XML standard for bioinformatics documents that
> allows us to catalog them in our database. Once XML takes over the
> Internet we release a web-crawler that updates the database
> automagically. Then we sit back and get rich and fat.
************************************************************************
Alan Williams
------------------------------------------------------------------------
University of California, Riverside "Where observation is concerned,
Dept. of Botany and Plant Sciences chance favors the prepared mind."
Alan@TheWilliamsFamily.org -- Louis Pasteur
************************************************************************
From finklesk at Op.Net Mon Jul 19 11:48:24 1999
From: finklesk at Op.Net (NNY)
Date: Fri Feb 10 19:18:45 2006
Subject: [Pipet Devel] GtkGLArea gets Python wrapper
In-Reply-To: <379304EB.8EAA2327@bc.edu>
Message-ID:
hi!
maybe i missed out on this before... i gather from this that you want
everything to be written in python? if whatever you want me to do is to be
written in python, where can i find more info on python programming?
-greg
http://www.op.net/~finklesk/index.html
"The problem is not that the world is full of fools. The problem is that
lightning isn't being distributed right." - Mark Twain
On Mon, 19 Jul 1999, J.W. Bizzaro wrote:
> Locians,
>
> Very good news:
>
> James Henstridge writes:
>
> > In other news, I have added a wrapper for gtkglarea to pygtk. There are a
> > few examples in the examples/gl directory, including a translation of the
> > mesa gears demo. To use it, you will also need the PyOpenGL package.
>
> GtkGLArea is the Gtk drawing area/widget for OpenGL:
>
> http://www.student.oulu.fi/~jlof/gtkglarea/
>
> I wrote to James about making a Python wrapper for it, and well, he just did.
> The bottom line for us is that we can make Python-based widgets for Loci to
> render 3D models. Very cool. This brings us another step closer to integrating
> AMMP and MMTk.
>
>
> Cheers.
> Jeff
> --
> +------------------------------------+
> | |
> | J.W. Bizzaro |
> | jeff@bioinformatics.org |
> | |
> | THE OPEN COLLABORATORY |
> | FOR MOLECULAR BIOINFORMATICS |
> | |
> | http://bioinformatics.org/ |
> | |
> +------------------------------------+
>
> _______________________________________________
> pipet-devel maillist - pipet-devel@bioinformatics.org
> http://bioinformatics.org/mailman/listinfo/pipet-devel
>
>
From bizzaro at bc.edu Tue Jul 20 02:05:01 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:45 2006
Subject: [Pipet Devel] GtkGLArea gets Python wrapper
References:
Message-ID: <3794118D.554520F8@bc.edu>
NNY wrote:
>
> maybe i missed out on this before... i gather from this that you want
> everything to be written in python?
Hi Greg. The confusion comes from the fact that Loci's design has been changing
so much, as has been the role of Python. At one point I might have said we
should strive for 100% Python, and use C only if we really have to. But
recently some of us, particularly Justin, Humberto and Alan, have put the CORBA
(and other object models) option back on the table. The greatest advantage of
using these models is perhaps language-independence. So, Python will not always
be REQUIRED for Loci development.
Where does Python stand in the big picture now? Well, it will always play a
major role doing what it does extremely well: acting as a glue and scripting
language for Loci. We plan to make the major GUI components, such as the
Workspace, in Python-GTK. BUT, CORBA et al will allow us to make non-Python
plug-ins/widgets/loci.
Depending on the uniqueness of the widget/locus, use of Python will be more or
less a part of making one. For example, if a widget/locus outputs to a
GtkGLArea canvas, the widget/locus can call it via CORBA, and it probably won't
need any Python wrappers. But if the widget/locus needs a custom drawing area,
we'll have to use Python to put it in the Workspace.
> if whatever you want me to do is to be
> written in python, where can i find more info on python programming?
You'll find some links about learning Python-Gtk/Gnome at the PyG Tools page:
http://bioinformatics.org/pygtools/
You can also check out the Python page:
http://www.python.org/
A REALLY good book, if you want to go that route, is
Learning Python
Mark Lutz and David Ascher
O'Reilly, 1999
ISBN 1-56592-464-9
But what was I hoping you could do for Loci? After all, I asked you to help;
you didn't volunteer. We need a molecule modeling widget/locus for starters: a
plug-in that can render 3D, OpenGL molecules. Fortunately, we have two
complementary projects to base this on. Rob Harrison has much of the C code to
display molecules. His program is AMMP (Another Molecular Modeling Program):
http://asterix.jci.tju.edu/ammp.html
And of course you have your mg^2 modeler and experience with OpenGL. I think we
can combine much of what we have into a widget/locus without a lot of new code.
Will this require Python? I think we can either use the Python-GtkGLArea
wrapper or make it all in C and then write our own wrapper. But if we make a
Python-based widget/locus, we'll have more reuse.
Cheers.
Jeff
>
> -greg
>
> http://www.op.net/~finklesk/index.html
>
> "The problem is not that the world is full of fools. The problem is that
> lightning isn't being distributed right." - Mark Twain
>
> On Mon, 19 Jul 1999, J.W. Bizzaro wrote:
>
> > Locians,
> >
> > Very good news:
> >
> > James Henstridge writes:
> >
> > > In other news, I have added a wrapper for gtkglarea to pygtk. There are a
> > > few examples in the examples/gl directory, including a translation of the
> > > mesa gears demo. To use it, you will also need the PyOpenGL package.
> >
> > GtkGLArea is the Gtk drawing area/widget for OpenGL:
> >
> > http://www.student.oulu.fi/~jlof/gtkglarea/
> >
> > I wrote to James about making a Python wrapper for it, and well, he just did.
> > The bottom line for us is that we can make Python-based widgets for Loci to
> > render 3D models. Very cool. This brings us another step closer to integrating
> > AMMP and MMTk.
> >
> >
> > Cheers.
> > Jeff
--
+------------------------------------+
| |
| J.W. Bizzaro |
| jeff@bioinformatics.org |
| |
| THE OPEN COLLABORATORY |
| FOR MOLECULAR BIOINFORMATICS |
| |
| http://bioinformatics.org/ |
| |
+------------------------------------+
From bizzaro at bc.edu Tue Jul 20 08:19:35 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:45 2006
Subject: [Pipet Devel] Re: The Loci Project
References: <199907110811.KAA14566@pcisrec-d402b.unil.ch>
Message-ID: <37946957.AC8FD765@bc.edu>
Hello Thomas.
I'm sorry that I took so long to get back to you.
Thomas Junier wrote:
>
> All I can say is that I'm very pleased, but I sincerely wonder if I can be of
> any help, because I know close to nothing about Python (I'm more of the C/Perl/
> Java world), as to CORBA, DOM and XML I have some idea about what they do, but
> not much. Of course, I could start learning all this. :-)
Python is being used as a glue language for Loci. Knowledge of it would be
helpful but should not be required. We are aiming for a language-neutral
system, a la CORBA. So, we're not forcing anyone to pick up a book on Python
and start reading ;-)
> > I
> > think what you have done is an important building block for Loci.
>
> Well, I'm all the more pleased, but since it's based on Perl and Java, won't it
> be hard to integrate it into Loci ?
Regarding language, as long as a "translator" can connect to CORBA, the language
shouldn't matter. If we use SEView (or a derivative), we will have to work
these object models into it.
I think we could also use your help with defining a generic "translator" for
I/O. The definition should be such that someone can write one in the language
of their choosing. We can take a look at SEView and make sort of a generic
algorithm that can be used as a blueprint. (That might even be publishable.)
> So my answer is that I'm interested, but I'm not sure how I can be useful. If I
> first have to learn Python, CORBA, XML and friends, it'll be some time before I
> can be productive, I'm afraid. On the other hand, if my Perl/C/Java skills can
> be put to use, that would allow me to start working sooner.
Well, most of us will need a lesson in CORBA. C works well with Python, and
we're sure to have a bit of it in Loci. Actually, most Loci developers are C
coders and only a few joined knowing Python, CORBA, etc. We have a few Perl
hackers here too, but Python has some obvious strengths for what we need to do.
> One thing I could not find on the Loci page: what kind of collaboration do you
> have with EMBOSS ?
Peter Rice, the coordinator of EMBOSS, reads our list and I read theirs. (He's
sure to read this :-) And we've corresponded a few times, but that's about it.
If I can take the liberty to speak for them, they are developing a command-line
based system much in the spirit of the GCG Wisconsin Package. They have chosen
not to choose a GUI because there are several existing that can interface with
the EMBOSS command-line (Loci could be on that list but doesn't really
"exist"). We would like to make translators (here's where you guys come in) to
interface EMBOSS with Loci, but EMBOSS has taken no official position on Loci.
BTW, have you spoken to Philipp about Loci? I did not get a message back from
him. Does he still work with you?
Would you like to join our mailing list?
http://bioinformatics.org/mailman/listinfo/pipet-devel/
I can also make an account for you on our server.
Cheers.
Jeff
--
+------------------------------------+
| |
| J.W. Bizzaro |
| jeff@bioinformatics.org |
| |
| THE OPEN COLLABORATORY |
| FOR MOLECULAR BIOINFORMATICS |
| |
| http://bioinformatics.org/ |
| |
+------------------------------------+
From bizzaro at bc.edu Tue Jul 20 08:30:36 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:45 2006
Subject: [Pipet Devel] BioInfo (was: PHP is up)
References:
Message-ID: <37946BEC.21DCE3DF@bc.edu>
"Alan J. Williams" wrote:
>
> Along these lines, I have started to put together a bioinformatics and
> molecular biology jump site at www.molbio.org. Currently the only thing
> up and running is the news service. It allows for posting to molbio.org
> by anyone from the web. I want to add a catalog of web resources that can
> be updated by anyone from the web before I announce the site, which is why
> I haven't mentioned it to date.
I just took a peek at what you have, and it looks very nice. Are you planning
on selling advertising?
BioInfo will probably become a portal but more specific to bioinformatics. We
are looking to add longer feature articles/editorials, Yahoo!-like links pages
(BioWho? or BioHoo!), and I think an events calendar would be nice too.
Let me know when you are ready to announce molbio.org and I'll post it on
BioInfo.
Cheers.
Jeff
>
> On Sun, 18 Jul 1999, Gary Van Domselaar wrote:
> > > What do you think should be in a bioinformatics portal?
> >
> > TOL's bioinfo is _exactly_ what I was thinking ;-) Add hot current
> > events in bioinformatics with a hierachically organized database like
> > yahoo. Then we pass an XML standard for bioinformatics documents that
> > allows us to catalog them in our database. Once XML takes over the
> > Internet we release a web-crawler that updates the database
> > automagically. Then we sit back and get rich and fat.
>
--
+------------------------------------+
| |
| J.W. Bizzaro |
| jeff@bioinformatics.org |
| |
| THE OPEN COLLABORATORY |
| FOR MOLECULAR BIOINFORMATICS |
| |
| http://bioinformatics.org/ |
| |
+------------------------------------+
From pmr at sanger.ac.uk Tue Jul 20 10:44:24 1999
From: pmr at sanger.ac.uk (Peter Rice)
Date: Fri Feb 10 19:18:45 2006
Subject: [Pipet Devel] Re: The Loci Project
In-Reply-To: <37946957.AC8FD765@bc.edu> (bizzaro@bc.edu)
References: <199907110811.KAA14566@pcisrec-d402b.unil.ch> <37946957.AC8FD765@bc.edu>
Message-ID: <199907201444.OAA23090@unst.sanger.ac.uk>
Jeff Bizarro wrote:
>Thomas Junier wrote:
>> One thing I could not find on the Loci page: what kind of
>> collaboration do you have with EMBOSS ?
>Peter Rice, the coordinator of EMBOSS, reads our list and I read
>theirs. (He's sure to read this :-) And we've corresponded a few
>times, but that's about it.
Yup, I'm here :-)
>If I can take the liberty to speak for them, they are developing a
>command-line based system much in the spirit of the GCG Wisconsin
>Package. They have chosen not to choose a GUI because there are
>several existing that can interface with the EMBOSS command-line
>(Loci could be on that list but doesn't really "exist"). We would
>like to make translators (here's where you guys come in) to interface
>EMBOSS with Loci, but EMBOSS has taken no official position on Loci.
EMBOSS appears to be command line based, but internally it uses a
simple "AJAX command definition" file (the idea comes from VMS). These
"ACD" files can be converted to other GUI definitions, so that we hope
to automate implementing EMBOSS under most other GUIs in
bioinformatics.
There are many of these around the EMBnet community and
beyond. Examples are BioNavigator (eBioinformatics and EMBnet
Australia) AppLab (Martin Senger, EBI), W2H (Martin Senger and EMBnet
Germany), www2gcg (EMBnet Belgium), SRS applications (EBI and Lion),
ACEDB utilities (Sanger Centre and Montpelier), Staden (Rodger Staden,
Cambridge), SeqPup (Don Gilbert, Indiana). No doubt there are others
and I would be interested to hear of your favourites. Each has its own
definition format, but all have similar content.
ACD files define everything that an application needs, and have
extensions which EMBOSS ignores to allow HTML forms and other GUIs to
be specified. These are very easy to extend.
--
----------------------------------------------------------------------
Peter Rice | Informatics Division, The Sanger Centre,
E-mail: pmr@sanger.ac.uk | Wellcome Trust Genome Campus,
Tel: (44) 1223 494967 | Hinxton, Cambridge, CB10 1SA, England
Fax: (44) 1223 494919 | URL: http://www.sanger.ac.uk/Users/pmr/
From finklesk at Op.Net Tue Jul 20 23:44:27 1999
From: finklesk at Op.Net (NNY)
Date: Fri Feb 10 19:18:45 2006
Subject: [Pipet Devel] GtkGLArea gets Python wrapper
In-Reply-To: <3794118D.554520F8@bc.edu>
Message-ID:
sounds fine. i'll look into AMMP. i'm on standby. wake me when you want me
to do some coding :)
later
-greg
http://www.op.net/~finklesk/index.html
"The problem is not that the world is full of fools. The problem is that
lightning isn't being distributed right." - Mark Twain
On Tue, 20 Jul 1999, J.W. Bizzaro wrote:
> NNY wrote:
> >
> > maybe i missed out on this before... i gather from this that you want
> > everything to be written in python?
>
> Hi Greg. The confusion comes from the fact that Loci's design has been changing
> so much, as has been the role of Python. At one point I might have said we
> should strive for 100% Python, and use C only if we really have to. But
> recently some of us, particularly Justin, Humberto and Alan, have put the CORBA
> (and other object models) option back on the table. The greatest advantage of
> using these models is perhaps language-independence. So, Python will not always
> be REQUIRED for Loci development.
>
> Where does Python stand in the big picture now? Well, it will always play a
> major role doing what it does extremely well: acting as a glue and scripting
> language for Loci. We plan to make the major GUI components, such as the
> Workspace, in Python-GTK. BUT, CORBA et al will allow us to make non-Python
> plug-ins/widgets/loci.
>
> Depending on the uniqueness of the widget/locus, use of Python will be more or
> less a part of making one. For example, if a widget/locus outputs to a
> GtkGLArea canvas, the widget/locus can call it via CORBA, and it probably won't
> need any Python wrappers. But if the widget/locus needs a custom drawing area,
> we'll have to use Python to put it in the Workspace.
>
> > if whatever you want me to do is to be
> > written in python, where can i find more info on python programming?
>
> You'll find some links about learning Python-Gtk/Gnome at the PyG Tools page:
>
> http://bioinformatics.org/pygtools/
>
> You can also check out the Python page:
>
> http://www.python.org/
>
> A REALLY good book, if you want to go that route, is
>
> Learning Python
> Mark Lutz and David Ascher
> O'Reilly, 1999
> ISBN 1-56592-464-9
>
> But what was I hoping you could do for Loci? After all, I asked you to help;
> you didn't volunteer. We need a molecule modeling widget/locus for starters: a
> plug-in that can render 3D, OpenGL molecules. Fortunately, we have two
> complementary projects to base this on. Rob Harrison has much of the C code to
> display molecules. His program is AMMP (Another Molecular Modeling Program):
>
> http://asterix.jci.tju.edu/ammp.html
>
> And of course you have your mg^2 modeler and experience with OpenGL. I think we
> can combine much of what we have into a widget/locus without a lot of new code.
> Will this require Python? I think we can either use the Python-GtkGLArea
> wrapper or make it all in C and then write our own wrapper. But if we make a
> Python-based widget/locus, we'll have more reuse.
>
>
> Cheers.
> Jeff
>
>
> >
> > -greg
> >
> > http://www.op.net/~finklesk/index.html
> >
> > "The problem is not that the world is full of fools. The problem is that
> > lightning isn't being distributed right." - Mark Twain
> >
> > On Mon, 19 Jul 1999, J.W. Bizzaro wrote:
> >
> > > Locians,
> > >
> > > Very good news:
> > >
> > > James Henstridge writes:
> > >
> > > > In other news, I have added a wrapper for gtkglarea to pygtk. There are a
> > > > few examples in the examples/gl directory, including a translation of the
> > > > mesa gears demo. To use it, you will also need the PyOpenGL package.
> > >
> > > GtkGLArea is the Gtk drawing area/widget for OpenGL:
> > >
> > > http://www.student.oulu.fi/~jlof/gtkglarea/
> > >
> > > I wrote to James about making a Python wrapper for it, and well, he just did.
> > > The bottom line for us is that we can make Python-based widgets for Loci to
> > > render 3D models. Very cool. This brings us another step closer to integrating
> > > AMMP and MMTk.
> > >
> > >
> > > Cheers.
> > > Jeff
>
> --
> +------------------------------------+
> | |
> | J.W. Bizzaro |
> | jeff@bioinformatics.org |
> | |
> | THE OPEN COLLABORATORY |
> | FOR MOLECULAR BIOINFORMATICS |
> | |
> | http://bioinformatics.org/ |
> | |
> +------------------------------------+
>
> _______________________________________________
> pipet-devel maillist - pipet-devel@bioinformatics.org
> http://bioinformatics.org/mailman/listinfo/pipet-devel
>
>
From bizzaro at bc.edu Wed Jul 21 10:22:59 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:45 2006
Subject: [Pipet Devel] some info on Gnome
Message-ID: <3795D7C3.ECF0A184@bc.edu>
Locians,
I came across some articles at the "RedHat Knowledge Base" about Gnome. (I
think they come from the "whitepapers".) A few of these may be good to read if
you want an introduction to some of the Gnome technologies we are planning on
using in Loci:
Gnome Technologies
http://www.redhat.com/knowledgebase/gtg/
Gnome Components
http://www.redhat.com/knowledgebase/Components/
CORBA and Gnome
http://www.redhat.com/knowledgebase/ORBit/
Gnome Canvas
http://www.redhat.com/knowledgebase/canvas/
Cheerios.
Jeff
--
+------------------------------------+
| |
| J.W. Bizzaro |
| jeff@bioinformatics.org |
| |
| THE OPEN COLLABORATORY |
| FOR MOLECULAR BIOINFORMATICS |
| |
| http://bioinformatics.org/ |
| |
+------------------------------------+
From bizzaro at bc.edu Thu Jul 22 06:19:18 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:45 2006
Subject: [Pipet Devel] GTKML
Message-ID: <3796F026.5B5B1C4C@bc.edu>
Locians,
I came across another XML for defining a Gtk GUI. It is not related to
GLADE/XML, which I had been planning on using to define locus GUI's, but we're
sure to glean some more knowledge from this. Here is a short description and
the URL:
GTKML stands for "GTK Markup Language". Its purpose is to create an XML document
format for defining GTK-based user interfaces. The benefits of such a standard
would include that any GTKML-compliant language binding/framework could be used
with any GTKML-compliant visual editor, rapid application development, end-users
of an application can edit/alter/extend the user-interface without altering
code, end-users can easily create language-translations of GTKML documents and
share them with others, and more.
http://www.k-3d.com/index_gtkml.html
:-)
Jeff
--
+------------------------------------+
| |
| J.W. Bizzaro |
| jeff@bioinformatics.org |
| |
| THE OPEN COLLABORATORY |
| FOR MOLECULAR BIOINFORMATICS |
| |
| http://bioinformatics.org/ |
| |
+------------------------------------+
From bizzaro at bc.edu Sun Jul 25 12:14:29 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:45 2006
Subject: [Pipet Devel] dbXML
Message-ID: <379B37E5.FEA5435E@bc.edu>
Locians,
I found an announcement for the dbXML project at Freshmeat. This appears to be
what we were discussing a short while ago: If we're using all XML for our data,
why not use an XML-based database? Well, we weren't aware of any at the time.
Here's the announcement (Justin, is this guy related to you?):
dbXML project now online
Tom Bradford - July 22nd 1999, 04:55 EST
The dbXML project is a development effort with the ultimate goal of
producing a high-performance client/server DBMS for XML-based
structured documents. Overall, the theory is that you could speed up
database retrieval incredibly if you did not have to join tables
constantly to retrieve structured data. So many programs are written
to import and export tabular query results to and from XML that it
seems like somewhat of a useless step. Why not just store entire
structured documents as single entities and retrieve whole or partial
documents with simple SQL queries? This is the goal of the dbXML
project. The project is only a little more than one week old and is
actively looking for talented volunteer contributors.
http://www.dbxml.org
They are looking for help. Maybe we can kill two birds with one stone here.
:-)
Jeff
--
+------------------------------------+
| |
| J.W. Bizzaro |
| jeff@bioinformatics.org |
| |
| THE OPEN COLLABORATORY |
| FOR MOLECULAR BIOINFORMATICS |
| |
| http://bioinformatics.org/ |
| |
+------------------------------------+
From justin at ukans.edu Sun Jul 25 19:14:23 1999
From: justin at ukans.edu (Justin Bradford)
Date: Fri Feb 10 19:18:45 2006
Subject: [Pipet Devel] dbXML
In-Reply-To: <379B37E5.FEA5435E@bc.edu>
Message-ID:
> If we're using all XML for our data,
> why not use an XML-based database? Well, we weren't aware of any at
> the time.
> Here's the announcement (Justin, is this guy related to you?):
Yeah. I've been looking at various XML databases, search engines, query
languages, etc. I missed this one, however, but I'll take a look at it, as
we'll ultimately want something like this.
> Tom Bradford - July 22nd 1999, 04:55 EST
Hey, this guy has my last name, too.
Justin
From gvd at redpoll.pharmacy.ualberta.ca Mon Jul 26 03:18:05 1999
From: gvd at redpoll.pharmacy.ualberta.ca (Gary Van Domselaar)
Date: Fri Feb 10 19:18:45 2006
Subject: [Pipet Devel] Web Page Update
Message-ID: <199907260718.BAA05803@redpoll.pharmacy.ualberta.ca>
Locians,
As you may know, I have been working on upgrading the web server with
PHP. I recently installed the mysql relational database on theopenlab
box, so now we can use PHP with mysql (joy!). Jeff pointed out a
cst-calendar proggy that uses mysql with php. i installed it on my home
box:
http://gvd.v-wave.com/~gvd/calendar/index.php3
if you like it i can instal it on the openlab server for the bioinfo portal.
I had a little bit of trouble turning on the server-side includes for
theopenlab apache server, this resulted in a 'broken' stats page and
counter. I personally am not too fond of the web stats generator that
was being used (big brother): it logs and displays visitor information
like operationg system and stuff-- good stuff for script kiddies. for
your consideration i put the webalizer on there instead. Just click the
'view the statistics' link at the bottom of theopenlab main page to check
it out. Big brother is still there, but if you want to view it i suggest
to password protect it first.
I also placed a php/sql counter on theopenlab index and loci index
pages. If you like them i will keep them. I think they look fine.
Finally, I have begun working on a template for the new web page design.
point your browser to
http://bioinformatics.org/dev/
and tell me what you think (its still very rough).
--Gary
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Gary Van Domselaar gvd@redpoll.pharmacy.ualberta.ca
Faculty of Pharmacy Phone: (780) 492-4493
University of Alberta FAX: (780) 492-5305
Edmonton, Alberta, Canada
From bizzaro at bc.edu Mon Jul 26 06:30:11 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:45 2006
Subject: [Pipet Devel] Re: Web Page Update
References: <199907260718.BAA05803@redpoll.pharmacy.ualberta.ca>
Message-ID: <379C38B3.222E07B6@bc.edu>
Hi Gary!
I guess you just answered my question about Webalizer, and I was also wondering
what happened to BigBro Stats :-)
Gary Van Domselaar wrote:
>
> As you may know, I have been working on upgrading the web server with
> PHP. I recently installed the mysql relational database on theopenlab
> box, so now we can use PHP with mysql (joy!).
Great. Thank you!
> Jeff pointed out a
> cst-calendar proggy that uses mysql with php. i installed it on my home
> box:
> http://gvd.v-wave.com/~gvd/calendar/index.php3
> if you like it i can instal it on the openlab server for the bioinfo portal.
I think it lacks a whole-year view. It would be nice if there were clickable
"horizontal bars" in such a view showing the duration of a long event like a
conference. Do you know what I mean? Do you know of any other calendars?
Maybe we can request this feature.
> I had a little bit of trouble turning on the server-side includes for
> theopenlab apache server, this resulted in a 'broken' stats page and
> counter. I personally am not too fond of the web stats generator that
> was being used (big brother): it logs and displays visitor information
> like operationg system and stuff-- good stuff for script kiddies. for
> your consideration i put the webalizer on there instead. Just click the
> 'view the statistics' link at the bottom of theopenlab main page to check
> it out. Big brother is still there, but if you want to view it i suggest
> to password protect it first.
Oh. I didn't think it was a security problem, but I guess you know more about
that than I do. Webalizer looks nice. As long as I/we can get an idea as to
what the activity is on the server.
> I also placed a php/sql counter on theopenlab index and loci index
> pages. If you like them i will keep them. I think they look fine.
They look fine to me too.
> Finally, I have begun working on a template for the new web page design.
>
> point your browser to
> http://bioinformatics.org/dev/
> and tell me what you think (its still very rough).
I like the title and the background. The background looks like a Bowie Poag
image; is it? I don't think the menu area color (robin's egg?) matches the
background though. BTW, did you catch the tag that goes in the body?
The news program actually generates index.shtml from index.template.
goes in index.template. I still need to post my logo idea too. Anyone else
have an idea for a logo? Nice work, Gary. Thank you.
:-)
Jeff
--
+------------------------------------+
| |
| J.W. Bizzaro |
| jeff@bioinformatics.org |
| |
| THE OPEN COLLABORATORY |
| FOR MOLECULAR BIOINFORMATICS |
| |
| http://bioinformatics.org/ |
| |
+------------------------------------+
From David.Lapointe at umassmed.edu Mon Jul 26 10:22:07 1999
From: David.Lapointe at umassmed.edu (Lapointe, David)
Date: Fri Feb 10 19:18:45 2006
Subject: [Pipet Devel] dbXML
Message-ID: <93307F07DE63D211B2F30000F808E9E501644D47@edunivexch02.umassmed.edu>
Along these lines, this may be of interest.
http://www.w3.org/XML/RDB.html
David Lapointe
Manager - Research Computing Services
UMass Medical School
Worcester, MA 01655
508/856-5141
> -----Original Message-----
> From: J.W. Bizzaro [mailto:bizzaro@bc.edu]
> Sent: Sunday, July 25, 1999 12:14 PM
> To: pipet-devel
> Subject: [Pipet Devel] dbXML
>
>
> Locians,
>
> I found an announcement for the dbXML project at Freshmeat.
> This appears to be
> what we were discussing a short while ago: If we're using all
> XML for our data,
> why not use an XML-based database? Well, we weren't aware of
> any at the time.
> Here's the announcement (Justin, is this guy related to you?):
>
> dbXML project now online
> Tom Bradford - July 22nd 1999, 04:55 EST
>
> The dbXML project is a development effort with the ultimate goal of
> producing a high-performance client/server DBMS for XML-based
> structured documents. Overall, the theory is that you
> could speed up
> database retrieval incredibly if you did not have to join tables
> constantly to retrieve structured data. So many programs
> are written
> to import and export tabular query results to and from XML that it
> seems like somewhat of a useless step. Why not just store entire
> structured documents as single entities and retrieve whole
> or partial
> documents with simple SQL queries? This is the goal of the dbXML
> project. The project is only a little more than one week old and is
> actively looking for talented volunteer contributors.
>
http://www.dbxml.org
They are looking for help. Maybe we can kill two birds with one stone here.
:-)
Jeff
--
+------------------------------------+
| |
| J.W. Bizzaro |
| jeff@bioinformatics.org |
| |
| THE OPEN COLLABORATORY |
| FOR MOLECULAR BIOINFORMATICS |
| |
| http://bioinformatics.org/ |
| |
+------------------------------------+
_______________________________________________
pipet-devel maillist - pipet-devel@bioinformatics.org
http://bioinformatics.org/mailman/listinfo/pipet-devel
From gvd at redpoll.pharmacy.ualberta.ca Mon Jul 26 15:51:02 1999
From: gvd at redpoll.pharmacy.ualberta.ca (Gary Van Domselaar)
Date: Fri Feb 10 19:18:45 2006
Subject: [Pipet Devel] Re: Web Page Update
References: <199907260718.BAA05803@redpoll.pharmacy.ualberta.ca> <379C38B3.222E07B6@bc.edu>
Message-ID: <379CBC25.54934859@redpoll.pharmacy.ualberta.ca>
J.W. Bizzaro wrote:
>
>
> I like the title and the background. The background looks like a Bowie Poag
> image; is it?
It most definitely is-- the latest from the Redmond Invasion Tour.
> I don't think the menu area color (robin's egg?) matches the
> background though.
Oh i know.. I'll make something nicer looking as things progress.
> BTW, did you catch the tag that goes in the body?
> The news program actually generates index.shtml from index.template.
> goes in index.template.
My design proposal for the pages is to use php to create a shell file. The file
will "include" the header (logo, background image, etc.) from a standard file.
The Menu will be generated dynamically from a php script (using catalog
information included in each individual web page) and placed into the menu table,
which can be on the right or left. The main text will again be grabbed from a
file, so if i grab index.shtml, which is generated from index.template using (what
news proggy are you using?), the most recently generated index.shtml will always
appear in the main panel.
Im making use of cascading style sheets to format the web pages, so once we have a
nice looking template page, applying the style to the existing pages should be a
snap.
--Gary
From bizzaro at bc.edu Mon Jul 26 18:07:27 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:45 2006
Subject: [Pipet Devel] Re: Web Page Update
References: <199907260718.BAA05803@redpoll.pharmacy.ualberta.ca> <379C38B3.222E07B6@bc.edu> <379CBC25.54934859@redpoll.pharmacy.ualberta.ca>
Message-ID: <379CDC1F.9B6011F1@bc.edu>
Gary Van Domselaar wrote:
>
> > I don't think the menu area color (robin's egg?) matches the
> > background though.
>
> Oh i know.. I'll make something nicer looking as things progress.
BTW, you probably noticed that I have a different background for each page. The
way I put the text in a white table in the middle of the page allows us to use
any busy pattern for the background around it. The effect is rather like a
window on a computer desktop. I was wondering if we could have a randomly
selected background. Perhaps PHP can do this?
Also, I am a bit fond of the "cartoon" theme I was starting with but didn't
quite implement. Check out the PyGTools page:
http://bioinformatics.org/pygtools/
See how the black outlines make it look a little cartoony? I just needed to
make some more drawings. Something to think about. But since you're doing the
work, you have the say.
> > BTW, did you catch the tag that goes in the body?
> > The news program actually generates index.shtml from index.template.
> > goes in index.template.
>
> My design proposal for the pages is to use php to create a shell file. The file
> will "include" the header (logo, background image, etc.) from a standard file.
> The Menu will be generated dynamically from a php script (using catalog
> information included in each individual web page) and placed into the menu table,
> which can be on the right or left. The main text will again be grabbed from a
> file, so if i grab index.shtml, which is generated from index.template using (what
> news proggy are you using?), the most recently generated index.shtml will always
> appear in the main panel.
The program is Htnews:
http://www.daemon.de/software.html
I can specify a "input/template" file and an "output" file; it doesn't matter
what they are called. Check out the /etc/htnews-* files on the system. So
whatever you want to "grab" the main text from, we can specify that as the
output file, which will come from a template file. It doesn't have to be named
the way it is now.
> Im making use of cascading style sheets to format the web pages, so once we have a
> nice looking template page, applying the style to the existing pages should be a
> snap.
Good. I hope I can follow all the new additions :-)
Cheers.
Jeff
--
+------------------------------------+
| |
| J.W. Bizzaro |
| jeff@bioinformatics.org |
| |
| THE OPEN COLLABORATORY |
| FOR MOLECULAR BIOINFORMATICS |
| |
| http://bioinformatics.org/ |
| |
+------------------------------------+
From bizzaro at bc.edu Mon Jul 26 18:54:42 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:45 2006
Subject: [Pipet Devel] workspace work
Message-ID: <379CE732.4B1930F1@bc.edu>
Locians,
Just to update you on the progress of programming Loci, there IS work being done
on the Workspace. I've been adding some versatility to the system. For
example, each locus can now have multiple inputs and outputs, whereas before
there was only one input per locus. I think each locus will have to specify all
of the inputs and outputs at the onset, and they'll be represented by
open/broken lines. The effect is a bit like placing a "bug" or little critter
on the Workspace, because the lines radiating from a geometric shape look like
legs on an insect. And the legs of one bug can be connected to another: output
is connected to input. Unconnected legs mean some information is missing or the
next step is unspecified, and this will likely mean the Workflow Diagram
won't..."flow". It's a good visual indicator anyway. Importantly, multiple
inputs allow us to have some complex control structures, such as loops, which
will make for a very powerful data processing system. I should have a snapshot
and a screenshot in a few days.
Cheers.
Jeff
--
+------------------------------------+
| |
| J.W. Bizzaro |
| jeff@bioinformatics.org |
| |
| THE OPEN COLLABORATORY |
| FOR MOLECULAR BIOINFORMATICS |
| |
| http://bioinformatics.org/ |
| |
+------------------------------------+
From bizzaro at bc.edu Wed Jul 28 23:12:50 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:45 2006
Subject: [Pipet Devel] an historical diversion
Message-ID: <379FC6B2.AACBDD60@bc.edu>
Greetings.
Since graphical user interfaces are of some importance to this project and a
special interest of mine, I thought I'd share a couple pics I came across today.
If you are familiar with the history of personal computers, you know the
importance of the work done by Xerox. If you are not, you may be surprised that
Apple did NOT invent the GUI. It is in fact well known that the Macintosh (and
the Lisa) GUI's were "ripped off" from the Xerox Alto. Here is a pic of the
Alto from circa late-1970's (yes, the 70's):
http://www.best.com/~curbow/xerox/alto.jpg
A sobering picture is that of the Xerox Star, which was introduced in 1981, 18
years ago!!!
http://www.best.com/~curbow/xerox/1/p10-lg.jpg
And of some interest to us, here is a picture of the Xerox Elixir desktop from
1990 (the pic is actually printed on a t-shirt). Notice the "process flow"
system, represented by icons connected with lines. Look familiar?
http://www.damer.com/pictures/elixir/products/shirt1m.jpg
Nine years ago. Hmmm.
:-)
Jeff
--
+------------------------------------+
| |
| J.W. Bizzaro |
| jeff@bioinformatics.org |
| |
| THE OPEN COLLABORATORY |
| FOR MOLECULAR BIOINFORMATICS |
| |
| http://bioinformatics.org/ |
| |
+------------------------------------+
From bizzaro at bc.edu Fri Jul 30 11:55:51 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:46 2006
Subject: [Pipet Devel] Thomas Junier joins!
Message-ID: <37A1CB07.140CBE73@bc.edu>
This is Thomas's reply to my message. He will be joining the project by helping
develop a model for translators/filters (programs that convert data from one
format to another). Recall that he and Philipp Bucher developed SEView. Jeff
-------------- next part --------------
An embedded message was scrubbed...
From: Thomas Junier
Subject: Re: The Loci Project
Date: Fri, 30 Jul 1999 13:19:53 +0200
Size: 3913
Url: http://bioinformatics.org/pipermail/pipet-devel/attachments/19990730/7ee388fc/attachment.mht
From bizzaro at bc.edu Sat Jul 31 18:26:47 1999
From: bizzaro at bc.edu (J.W. Bizzaro)
Date: Fri Feb 10 19:18:46 2006
Subject: [Pipet Devel] snapshots directory
Message-ID: <37A37827.3DA8DD1A@bc.edu>
My fellow Locians,
We'll be placing all development snapshots for Loci in a new Web directory on
the server:
http://bioinformatics.org/loci/download/snapshots/
This will give you a listing of all the snapshots available.
Adios.
Jeff
--
+------------------------------------+
| |
| J.W. Bizzaro |
| jeff@bioinformatics.org |
| |
| THE OPEN COLLABORATORY |
| FOR MOLECULAR BIOINFORMATICS |
| |
| http://bioinformatics.org/ |
| |
+------------------------------------+