Hello,

BeanExplorer is included into BDK as library in binary format:
plugins/com.beanexplorer_1.3.1/beanexplorer.jar
plugins/com.beanexplorer_1.3.1/beanhelpers.jar

There is special file src/build.xml that is included into BDK. It
allows to developer to build BioUML version from source files
using ant tool (http://ant.apache.org/).

You can type:

ant plugin.all

to build all BioUML plug-ins. Then you can start BioUML using run.bat
or shell.bat. Note: when you will start the application first time
then Eclipse runtime will build plug-ins registry (workspace
directory) and terminate the application, so you should start run.bat
again.

Please let me know if you will have some problems and other
questions.

With best regards,
Fedor.

--- In biouml@yahoogroups.com, "yuancheng02129" <yuancheng02129@y...>
wrote:
> Hi,
>
> I tried to build from the source. But beanexplorer class seems not
> in the source download and it is not open source at
> www.beanexplorer.com.  Is there any way I can get the source for
> free?  Thanks
>
>
> yc

Hi,

I tried to build from the source. But beanexplorer class seems not
in the source download and it is not open source at
www.beanexplorer.com.  Is there any way I can get the source for
free?  Thanks


yc

Dear friends,

abstracts, presentations and posters that were presented on different
conferences during 2003 are now available on line:

http://www.biouml.com/conferences.shtml

With best regards,
Fedor Kolpakov.

Dear friends,

first version of BioUML API documentation (raw and incomplete yet)
is available:
http://www.biouml.org/javadoc.shtml

BioUML workbench API documentation (v. 0.7.1) available in two
forms:

  - generated by javadoc
    (http://www.biouml.org/developer/javadoc/index.html);

  - generated by Together Control Center
    This version of documentation includes UML class diagrams
    for all packages.
   (http://www.biouml.org/developer/javadoc_together/index.html).

You also can download both versions of documentation as zip
files.
- http://www.biouml.org/download/0.7.1/javadoc.zip (3.03 mb)
- http://www.biouml.org/download/0.7.1/javadoc_together.zip (3.70 mb)

With best regards,
<br>Fedor.

Dear all,

New build (Build 20030920) of BioUML workbench have bee released.
http://www.biouml.org/download.shtml?0.7.1/download

This is support release that fixes some problems revealed in version
0.7.1 (beta):

MATLAB engine DLL loading error (fixed)
When user tries to start MATLAB engine from BioUML workbench it can
not find JMatLink.dll and prints following error message:
Error: Could not load the JMatLink library

SBW 1D array type (new)
New version allows to use 1D arrays as parameters of SBW service
methods. For this purpose JavaScript arrays (both JavaScript native
array and wrapped Java array) are converted into usual Java 1D
arrays. However this version does not supports 2D arrays and lists as
SBW service method parameters.

SBW host object help (corrected)
Some typos in help (description) of SBW host object functions are
corrected.

Load SBML model from file (new)
Possibility to load SBML model from file is added.
Here is an example:
model = sbw.loadModel("file",             // should be "file"
                       "c:/my_model.xml"); // model file nameÿ

With best regards,
Fedor.

I have got an error with version 0.7.1, that I didn't get with 0.7.0:


Error: Could not load the JMatLink library

Any idea what is wrong?

_________________________________________________________________
Få gode tilbud direkte i din mailbox http://jatak.msn.dk

Hello Casper,

There are following possibilities of using of SBML and MATLAB in
current version of BioUML:

SBML plug-in allows customer to use existing SBML models (they can be
imported as SBML module), edit them or create new ones. In SBML
module SBML format is used for model storage. Diagram layout is
stored using SBML <annotations> mechanism.
See http://www.biouml.org/plugin_sbml.shtml?overview for further
details.

MATLAB plug-in allows user to generate MATLAB files for SBML models
and BioUML standard simulation diagram type. For this purpose user
should open corresponding diagram, select MATLAB tab in right bottom
pane, specify MATLAB working directory, where generated files will be
stored and press 'Start MATLAB engine' button. The plug-in will
generate two files:

modelName_script.m
script file for model simulation and graphic results presentation

modelName_dy.m
function to calculate dy/dt for the model.

Then the plug-in will try to start the MATLAB and invoke the
generated script file for model simulation and results visualization.

Alternatively you can invoke SBW MatlabTranslator service to generate
corresponding MATLAB files for SBML models using JavaScript console.

In further we plan to provide conversion utility that will be able
convert content of standard BioUML pathway simulation diagram to SBML
format.

With best regards,
Fedor.

----------------------------------------------------------------------
These are examples of generated MATLAB files by MATLAB plug-in:

CellCycle_1991Gol_script.m
---------------------------
%script for 'CellCycle_1991Gol' model simulation

%constants declaration
global Reaction1_vi Reaction2_kd Reaction3_kd Reaction3_vd
Reaction4_K1 Reaction4_Kc Reaction4_VM1 Reaction5_K3 Reaction5_VM3
Reaction6_K2 Reaction6_V2 Reaction7_K4 Reaction7_V4 cytoplasm_EmptySet
Reaction1_vi = 0.023
Reaction2_kd = 0.00333
Reaction3_kd = 0.00333
Reaction3_vd = 0.1
Reaction4_K1 = 0.1
Reaction4_Kc = 0.3
Reaction4_VM1 = 0.5
Reaction5_K3 = 0.1
Reaction5_VM3 = 0.2
Reaction6_K2 = 0.1
Reaction6_V2 = 0.167
Reaction7_K4 = 0.1
Reaction7_V4 = 0.1

%Model boundary variables, they are declared as constants
cytoplasm_EmptySet = 0.0                % boundary variable
$cytoplasm.EmptySet

%Model rate variables and their initial values
y = []
y(1) = 0.0                              % y(1) - $cytoplasm.C
y(2) = 0.0                              % y(2) - $cytoplasm.M
y(3) = 0.0                              % y(3) - $cytoplasm.X

%numeric equation solving
[t,y] = ode23('CellCycle_1991Gol_dy',[0 100],y)

%plot the solver output
plot(t,y(:,1),'-',t,y(:,2),'-',t,y(:,3),'-')
title ('Solving Goldbeter problem')
ylabel ('y(t)')
xlabel ('x(t)')
legend('$cytoplasm.C','$cytoplasm.M','$cytoplasm.X');


CellCycle_1991Gol_dy.m
----------------------
function dy = CellCycle_1991Gol_dy(t, y)
% Calculates dy/dt for 'CellCycle_1991Gol' model.

%constants declaration
global Reaction1_vi Reaction2_kd Reaction3_kd Reaction3_vd
Reaction4_K1 Reaction4_Kc Reaction4_VM1 Reaction5_K3 Reaction5_VM3
Reaction6_K2 Reaction6_V2 Reaction7_K4 Reaction7_V4 cytoplasm_EmptySet

% write rules to calculate some eqution parameters
rateOfReaction1 = Reaction1_vi;
rateOfReaction2 = y(1)*Reaction2_kd;
rateOfReaction3 = (y(1)*Reaction3_vd*y(3))/(y(1) + Reaction3_kd);
rateOfReaction4 = ((1 - y(2))*Reaction4_VM1*y(1))/((1 + Reaction4_K1 -
  y(2))*(Reaction4_Kc + y(1)));
rateOfReaction5 = (Reaction5_VM3*(1 - y(3))*y(2))/(1 + Reaction5_K3 -
y(3));
rateOfReaction6 = (y(2)*Reaction6_V2)/(Reaction6_K2 + y(2));
rateOfReaction7 = (Reaction7_V4*y(3))/(Reaction7_K4 + y(3));


% calculates dy/dt for 'CellCycle-1991Gol.xml' model
dy = [  + rateOfReaction1 - rateOfReaction2 - rateOfReaction3
         + rateOfReaction4 - rateOfReaction6
         + rateOfReaction5 - rateOfReaction7]


--- In biouml@yahoogroups.com, "Casper Frederiksen" <in_silico@h...>
wrote:
> Hi Fedor,
>
>
> >I am not confident that I understood the question.
>
> Thanks. You understood the question correctly. Actually I thought
that you
> could save in SMBL or matlab, but as far as I can see that will be
included
> in a later version. It would also be nice with the possibility to
import
> SBML
>
>
> Regards,
>
> Casper
>
> _________________________________________________________________
> FÅ gode tilbud direkte i din mailbox http://jatak.msn.dk

Dear all,

New version of BioUML v. 0.7.1 have been released.
http://www.biouml.org/download.shtml?0.7.1/download

Main features that have been introduced in this version are:

- shell (command line) mode.
Now BioUML workbench can be started in headless using JavaScript
shell. This provides a simple way to run scripts in batch mode or an
interactive environment for exploratory programming.

- JavaScript custom functions and host objects.
JavaScript plug-in defines two extension points that allow other plug-
ins to expose their functions and objects to JavaScript shell.

JavaScript help
Using described above extension points developer can provide
description (documentation) for his functions and host objects. All
functions and host objects for which help description is available
will be shown in plug-in tree as children of JavaScript plug-in. When
corresponding function or host object will be selected, its
description will shown in Property Inspector pane. Alternatively user
can type function_name or help (function_name) and function
description will be printed in JavaScript shell.

SBW JavaScript host object
SBW host object provides tight integration between SBW and BioUML
JavaScript shell. Using this shell customer can write sophisticated
scripts for analyses and simulation of SBML models.

With best regards,
Fedor.

Hi Fedor,


>I am not confident that I understood the question.

Thanks. You understood the question correctly. Actually I thought that you
could save in SMBL or matlab, but as far as I can see that will be included
in a later version. It would also be nice with the possibility to import
SBML


Regards,

Casper

_________________________________________________________________
Få gode tilbud direkte i din mailbox http://jatak.msn.dk

Hello,

this version of KEGG module is suitable only for BioUML v. 0.5.
You can try to dowload BioUML v.0.5 and install KEGG module here.
http://www.biouml.com/download.shtml?0.5/download

We plan to release full-fledged version of KEGG module for BioUML
v.0.7 during October-November.

Wirh best regards,
Fedor.

--- In biouml@yahoogroups.com, "yuancheng02129" <yuancheng02129@y...>
wrote:
> Hi, there:
>
> I downloaded kegg.bmd (complete module) and imported into Biouml
> 0.7.0 as instructed.  There is a icon for kegg module showing up in
> left up window.  but there is no data at all.  Anything wrong with
> my download or import?  thanks
>
>
> yc

Hello Casper,

I am not confident that I understood the question.

In BioUML v. 0.7 diagrams are stored automatically when you
close the diagram or application.
Corresponding xml files located in
../biouml/data/module_name/diagrams directory.
You also can save open diagram using File->Save menu item
or File->Save As.

The only place where XSL template is mentioned is publishing
of BioUML diagram for the web Using File->Generate HTML menu item.
During this process gif image and map are generated and XSL template
is used to generate corresponding web pages and hyperlinks for gif
map. There was some xsl template TRANSPATH database, but it was not
included in standard distributive. Possibly I should hide this menu
until it is not completed.

With best regards,
Fedor.


--- In biouml@yahoogroups.com, "Casper Frederiksen" <in_silico@h...>
wrote:
>
> What .xsl file shoukld I use as template to save my diagrams?
>
>
> Regards,
>
> Casper
>
> _________________________________________________________________
> Få gode tilbud direkte i din mailbox http://jatak.msn.dk

Hi, there:

I downloaded kegg.bmd (complete module) and imported into Biouml
0.7.0 as instructed.  There is a icon for kegg module showing up in
left up window.  but there is no data at all.  Anything wrong with
my download or import?  thanks


yc

What .xsl file shoukld I use as template to save my diagrams?


Regards,

Casper

_________________________________________________________________
Få gode tilbud direkte i din mailbox http://jatak.msn.dk

Hi,

previously we have developed some test version
of KEGG module for BioUML v. 0.5.
http://www.biouml.com/download.shtml?0.5/download

direct link:
http://www.biouml.com/download/0.5/kegg_22.bmd

But it should be noted that the main goal of BioUML v. 0.5
was only to prove that the suggested approach can work
and to get some feedback from community.

With best regards,
Fedor Kolpakov.

--- In biouml@yahoogroups.com, "yuancheng02129" <yuancheng02129@y...>
wrote:
> Hi, all:
>
> I am a new comer to this group and Biouml.  I downloaded the v0.7.0
> and try to play with it.  The feature by which I was most fasinated
> is the database module.  But I could not find anywhere.  From the
> development roadmap, I learned that the database module won't be
> available until November this year. But from previous message,it
> seems to me that I can import module from, for example, kegg.bmd.
> My question is that where I can find kegg.bmd file. It seems
nowhere
> I can find kegg.bmd in my download.
>
> Thanks for all responses in advance.
>
>
> yuan cheng

Hi, all:

I am a new comer to this group and Biouml.  I downloaded the v0.7.0
and try to play with it.  The feature by which I was most fasinated
is the database module.  But I could not find anywhere.  From the
development roadmap, I learned that the database module won't be
available until November this year. But from previous message,it
seems to me that I can import module from, for example, kegg.bmd.
My question is that where I can find kegg.bmd file. It seems nowhere
I can find kegg.bmd in my download.

Thanks for all responses in advance.


yuan cheng

dear sir;

I am thankful to you for your quick response. I will
keep checking the site for the latest updates. Once i
get to know somw basic features of working of BioUML,
i feel i will be in a position to help you out in
preparing documentations and other help required by
you.

I would surely like to provide my extensive help to
you in preparing something which could be very useful
for others interested in this area.

Aditya

__________________________________
Do you Yahoo!?
Yahoo! SiteBuilder - Free, easy-to-use web site design software
http://sitebuilder.yahoo.com

Hello Aditya,

thank you for your interest to BioUML.

There are a few documentation for current version of BioUML
workbench. This is due to two reasons:

- now we are concentrated our efforts mainly on developing
new features and modules as well as on bug fixing;

- while BioUML workbench is in process of active development
the documentation should be updated frequently. So we will
prefer to complete current works that may affect on BioUML
workbench user interface and then provide needed help and
documentation.

We are planning to release next version (v. 0.7.1) during
next week and will try to provide some basic documentation:
how to create module, how to edit diagram and how to start
simulation.

While writing help and documentation is really big work that
can not be done during several days now we are prefer to
write documentation only for those modules and plug-ins that
are new in released version. So more detailed description
of JavaScript shell and integration with Systems Biology
Workbench (SBW) will be provided in v. 0.7.1.

I'll be glad to answer on your particular questions.

We would appreciate someone's volunteering to help us to
write some part of documentation or some tutorial for
BioUML.

Thanks,
Fedor.

--- In biouml@yahoogroups.com, "N.Aditya Sarma" <s_forn@y...> wrote:
> Hi friends;
>
> Hi i am Aditya. I am a new memebr to this group. I
> installed the bio uml product yesterday, at my work
> place. I tried to check things out in that, but i
> couldnt find any help files in that. I could figure
> out how i should run the product and moreover how i
> should invoke different utilites in that. If you could
> tell me a place where i can find a proper
> documentation, or may be a getting started user guide
> something like that, i would be thankful to you.
>
> I am working on Image Processing and pattern
> recognition of protein concentration in cells. Hope to
> get a reply from you very soon.
>
> Aditya

Hi friends;

Hi i am Aditya. I am a new memebr to this group. I
installed the bio uml product yesterday, at my work
place. I tried to check things out in that, but i
couldnt find any help files in that. I could figure
out how i should run the product and moreover how i
should invoke different utilites in that. If you could
tell me a place where i can find a proper
documentation, or may be a getting started user guide
something like that, i would be thankful to you.

I am working on Image Processing and pattern
recognition of protein concentration in cells. Hope to
get a reply from you very soon.

Aditya


__________________________________
Do you Yahoo!?
Yahoo! SiteBuilder - Free, easy-to-use web site design software
http://sitebuilder.yahoo.com

There was broken link to SBML models repository.

Now this link is correct:
http://www.biouml.com/module.shtml?sbml

With best regards,
Fedor.

Dear friends,

BioUML workbench source code is available as part
of BioUML Development Kit (BDK).

BDK allows to developer implement their own modules and extensions
for BioUML workbench as well as modify and improve BioUML workbench.
It includes all BioUML workbench source code as well as all necessary
third party libraries.

Makefile for Ant to compile and run BioUML workbench or it parts is
also provided.

With best regards,
Fedor Kolpakov

Dear friends,

We just have released new version of BioUML workbench:
http://www.biouml.org/download.shtml?0.7/release_notes

The main change in BioUML architecture is using of Eclipse
platform to provide BioUML workbench extensibility as well
as seamless integration with other tools for systems
biology.

Other major change is refactoring of our data types and
reaction concept to be compliant with SBML data types.
SBML version 1 level 1 is supported now:
http://www.biouml.org/plugin_sbml.shtml?overview

Additionally we have packed all models from SBML Model
Repository into BioUML module.
http://www.biouml.org/module.shtml?sbml_models

New diagram type for ontological description of some
biological process or system is introduced. This diagram
type is also convenient as overview.

Now arbitrary HTML text can be associated with the diagram
as its description. BioUML workbench provides simple editor
to edit the description as HTML or plain text.

It will be interesting to here your comments and suggestions
about this release.

Sincerely,
Fedor Kolpakov.

Dear Suraj,

Thank you for your interest to BioUML.

Slides 15-17 in "BioUML overview" presentation briefly demonstrate
main ideas of database search engine. Here you can get the
presentation:
http://www.biouml.com/presentations/biouml_overview.ppt

You also can download some intermediary version of BioUML:
http://www.biouml.com/download/0.55/install.exe
http://www.biouml.com/download/0.55/oro.jar

I forgot to include oro.jar into installer, so please download it
also and copy into directory where BioUML will be installed.
oro.jar allows customer to use regular expression (similar with Perl5)
in fiter fields. See the presentation for more details.

Now we are working on new version of BioUML (v. 0.7),
hopefully it will be available during this quarter.

I'll be glad to here any your comments or suggestions
to take them into account for further versions of BioUML.

Sincerely,
Fedor Kolpakov

=================================================================
--- In biouml@yahoogroups.com, "bio_informatician"
<bio_informatician@y...> wrote:
> Hi,
>
> I have downloaded the demo version of BioUML from the .org site.
The
> Query Screen for the individual database modules is disabled. Can
it
> be enabled? I would like to see the Query capabilities of BioUML.
>
> But for the Architecture diagram, Techincal details for BioUML is
not
> available. Can that be made availabe?
>
> Regards,
> Suraj.

Hi,

I have downloaded the demo version of BioUML from the .org site. The
Query Screen for the individual database modules is disabled. Can it
be enabled? I would like to see the Query capabilities of BioUML.

But for the Architecture diagram, Techincal details for BioUML is not
available. Can that be made availabe?

Regards,
Suraj.

Dear friends,

We register new domains dedicated to BioUML:
biouml.com, biouml.org and biouml.net.

Their provides the same content as www.biosoft.ru/biouml.net/.

Sincerely,
Fedor.

Hi Fedor,

Thank you very much.
Now I am able to see KEGG Pathway module running in BioUML framework.

Sincerely,
-Dattatraya Bhat

--- In biouml@y..., "Fedor Kolpakov" <fedor@D...> wrote:
> Here is a brief description how you can install BioUML module from
> *.bmd file, for example kegg.bmd.
> 'bmd' means BioUML Module Distributive.
>
> To install a new module you should select File -> Import module
> menu item. Then you can see a dialog to specify the module file,
> for example 'kegg.bmd'. After that you can see 'Module Info' dialog
> were you should check 'Accept' and press 'Continue' to go further.
> After that BioUML will start the module import which progress you
> can see in 'Import' dialog.
>
> After successful module import you can see new module in repository,
> for example after kegg.bmd import 'KEGG pathways' module will
> appear in repository tree.
>
> Sincerely,
> Fedor

Dear Dattatraya Bhat;

Now BioUML Development Kit that includes source code,
all needed libraries and makefile (build.xml for Ant) is available.
Using it you can build BioUML version from sources for your platform.

I hope we make installers for Unix platforms soon.

Sincerely,
Fedor

Here is a brief description how you can install BioUML module from
*.bmd file, for example kegg.bmd.
'bmd' means BioUML Module Distributive.

To install a new module you should select File -> Import module
menu item. Then you can see a dialog to specify the module file,
for example 'kegg.bmd'. After that you can see 'Module Info' dialog
were you should check 'Accept' and press 'Continue' to go further.
After that BioUML will start the module import which progress you
can see in 'Import' dialog.

After successful module import you can see new module in repository,
for example after kegg.bmd import 'KEGG pathways' module will
appear in repository tree.

Sincerely,
Fedor

Hi,

I have downloaded BioUML module -KEGG/pathways -complete module (1.4
mb) containing Java code and main data from KEGG/pathway database.

I am facing problem in intializing this
When I gave the following command in comand line:

D:\KEGGUMLTEST>java -jar kegg.jar

The message on the command line was:

Failed to load Main-Class manifest attribute from
kegg.jar

I request for the solution.

The other download BioUML framework Windows: (3.5 mb) is working fine.

Thanks
-Dattatraya Bhat

Hi,
Thanks for the development of BioUML
I would like to know when BioUML will be available for AIX and
Solaris flatforms

-Thanks
Dattatraya Bhat
Pune, India

Welcome to BioUML forum!

BioUML is intended to be common purpose visual language for
formalized graphic notation of molecular biological systems
structure and function as well as for they simulating.

The forum aims to promote and co-ordinate a community effort towards
of development and application of BioUML.

Here you can post your comments and suggestions related to BioUML.

Don't forget to visit BioUML site http://www.biosoft.ru/biouml.shtml
where you can find extensive information about BioUML and its latest
releases.

Thanks,
Fedor Kolpakov.