Dear colleagues,

New version of BioUML workbench have been released.
http://www.biouml.org/download.shtml?0.7.6/download

This is a brief overview of main features of new vesrion:

1. Preferences.
This version introduce new Preferences concept. It allows any plug-in
easily store its preferences
in XML file and provides dialog for preferences editing by a user.

2. Look and feels.
Currently BioUML workbench allows user to specify his favorite look
and feel and theme (if selected look and feel supports themes) using
Preferences dialog.
There is special extension point that allows a plug-in to contribute
new look and feels and their themes.

3. ODE solver for stiff problems.
New ODE solver for Java simulation engine was added.
It allows to solve stiff problems using Imex algorithm.
Additionally BioUML workbench now provides registry of available ODE
solvers and extension point that allows a plug-in developer
to contribute their ODE solvers to the registry.

4. User interface for rules and events.
Initial user interface was provided for creating and editing
rules and events. Currently it works only for BioULM "Pathway
simulation" diagram type, but will be adopted for SBML diagrams soon.

5. Performance improvements.
Loading and code generation for huge SBML models
have been optimised significantly.

With best regards,
BioUML team

Dear all,

Java documentation and class diagrams are generated for
BioUML workbench v. 0.7.5.
http://biouml.org/javadoc.shtml

With best regards,
Fedor.

Dear colleagues,

BioUML is the result of hard work of our team. Very often
this work is done on pure enthusiasm. And if you want BioUML
to become even better and more useful please consider
donating some money to support it:
http://www.biouml.org/donation.shtml

BioUML workbench is free and we want to keep it free open
source project. Your funds will help us to finance further
development and implement new exciting features, provide
support for new databases and formats (BioPax, GeneOntology,
CancerOntology, TRANSPATH, TRANSFAC, BIND, etc.)

There are also other ways to support BioUML development:

- contracts - your organisation could order development of new
feature or integration of their databases and software with BioUML
workbench;

- joint grants and projects - we will be glad to participate in joint
grants and projects that will allow us to develop BioUML or apply it
for modeling, simulation and analyses of complex systems;

- volunteers - we appreciate volunteers who will help us to write
user guide, help and documentation, as well as to integrate their
programs with BioUML workbench.

Thank you,
BioUML team

Dear colleagues,

New version of BioUML workbench have been released.

Main achievement of this version is that both simulation engines
(Java and MATLAB) provided by BioUML workbench v. 0.7.5 passed 100%
SBML semantic test suite. Test details available at:
http://www.biouml.org/sbml_tests/overview.html

This is a brief overview of main features that we introduced in this
version:

1. Simulation engine improvements
- Discontinuity (MathML piecewise) support
- Delay support
- Algebraic rules support
- Support of all MathML functions (factorial, sh, tgh, ctgh, ash,
atgh, etc.)

2. SBML semantic suite now is part of BDK (BioUML Development Kit).
Special package biouml.plugins.sbml._test contains Java code to start
SBML semantic tests and display results nicely.
Test details

3. Improved SBML support
- level 1 version 1 - read/write
- level 1 version 2 - read/write
- level 2 version 1 - read/write
- import SBML models as diagrams into other BioUML modules

4. Import - models in following formats now can be imported as
diagrams into other SBML modules:
- SBML
- CellML
- GINML (format used by GINsim framework - http://www.esil.univ-
mrs.fr/~chaouiya/GINsim/)

5. Export - diagrams can be exported in different formats
- PNG (Portable Network Graphic)
- JPEG
- BMP (bitmap)
- SVG (Scalable Vector Graphics - http://www.gupro.de/GXL/)
- GXL (Graph eXchange Language - http://www.gupro.de/GXL/)

6. New extension points
- diagramImport
- diagramExport

7. SBW 2.0.0 - new version of Systems Biology Workbench is used in
SBW plug-in.

BioUML simulation engines now are more or less stable and bugs free.
Now the main limitation is user interface that does not allows user
to utilize all power of simulation engine. Thus main priority for
next versions will be user interface enhancements.

Starting from this version we will try to follow XP (eXtreme
Programming) practices more thoroughly and release new versions more
frequently with smaller changes.

With best regards,
BioUML team

Hello,

yes, there is installer for Unix OS:
http://www.biouml.org/download/0.7.4/biouml.bin
http://www.biouml.org/download.shtml?0.7.4/download

We have tested this version for Linux, the only problem is MATLAB.
We are using special dll to run MATLAB on Windows, but we have not
MATLAB for Unix to reproduce the same functionality.
We appreciate if somebody will help us to adopt and test JMatlink for
Linux/Unix to launch MATLAB.

We also have tested BioUML on Mac. Diagram editor and other plug-ins
work normally, but simulation engines have problems:
- MATLAB - we need MATLAB version for Mac to write and test
JMatlink adapter for Mac.
- Java - java directories structure is significantly differ
for Mac and it is the problem to find tools.jar that allows
BioUML to launch javac to compile generated Java code.

Hopefully at January 10 we should release new version.
New version provides significantly improved Matlab and Java
simulation engines. Now they support algebraic equations, delay,
piece wise functions and all MathML functions.

Additinally we have tested improved Java and MATLAB simulation
engines using SBML semantic test suite:
http://sbml.org/wiki/Semantic_Test_Suite

Preliminary results of testing are available:
http://www.biouml.org/sbml_tests/overview.html

More information about further releases:
http://www.biouml.org/roadmap.shtml

With best regards,
Fedor

--- In biouml@yahoogroups.com, bio241247@m... wrote:
>
> Is there an installer available for BioUML workbench 0.7.4 (alpha)
or has it to be compiled from scratch ising the Unix version ?

Is there an installer available for BioUML workbench 0.7.4 (alpha) or has it to
be compiled from scratch ising the Unix version ?

I am still here.

i wan to join the development too.

but i have very little experience on programming java.

cheers.

--- In biouml@yahoogroups.com, "Greg" <gregory@c...> wrote:
> New member to last
>
> --- In biouml@yahoogroups.com, "pohyg" <pohyg@y...> wrote:
> > hi!
> >
> > I just got to know about this application.
> >
> > it seems to be fitting my needs model cells.
> >
> > I am wondering how many people actually used it? is it helpful in
> > research works?
> >
> > other than the listed team member developing it, is there any
> source
> > of developers who support the development of the application?
> >
> > Thanks.
>
> Are you still here?
> I am a developer and have chanced upon this.
>
> Greg

New member to last

--- In biouml@yahoogroups.com, "pohyg" <pohyg@y...> wrote:
> hi!
>
> I just got to know about this application.
>
> it seems to be fitting my needs model cells.
>
> I am wondering how many people actually used it? is it helpful in
> research works?
>
> other than the listed team member developing it, is there any
source
> of developers who support the development of the application?
>
> Thanks.

Are you still here?
I am a developer and have chanced upon this.

Greg

hi!

I just got to know about this application.

it seems to be fitting my needs model cells.

I am wondering how many people actually used it? is it helpful in
research works?

other than the listed team member developing it, is there any source
of developers who support the development of the application?

Thanks.

Dear yc,

Indeed it depends what you added.

If you simply added some new class or code to existing BioUML source
code then the simplest way will be to use ant (I am using ant version
1.5.3) and plugin.all target form build.xml as it was described in
the previous letter. If you have not experience with ant, please take
a look at http://ant.apache.org/manual/index.html, if you will have
some problems with it I will try to help.

If your code also provides some new extension point or implements
some extension you should also declare it in corresponding plugin.xml
file. We are using Eclipse platform runtime for this purpose. You can
find more information about Eclipse at: http://www.eclipse.org. If
you will provide me with more information
I will give you more concrete answer.

With best regards,
Fedor.

P.S. you can use my e-mail address: fedor@...

--- In biouml@yahoogroups.com, "yuancheng02129" <yuancheng02129@y...>
wrote:
> Hi, Fedor:
>
> Thanks for last message regarding beanexplorer classes. Now I have
> question about how to adopt them during compilation after I have
> changed (or add) something in other Biouml class source code and
> want to recompile them. Sorry for asking silly question. I am new
to
> Java world. Thanks.
>
> yc

Hi, Fedor:

Thanks for last message regarding beanexplorer classes. Now I have
question about how to adopt them during compilation after I have
changed (or add) something in other Biouml class source code and
want to recompile them. Sorry for asking silly question. I am new to
Java world. Thanks.

yc

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