Virtual Image for Corra and ATAQS are available for users who are not familiar with Unix installation.
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Mi-Youn Brusniak
Oct 31, 2011, 7:06:44 PM10/31/11
to co...@googlegroups.com
Dear Corra and ATAQS Users,
Based on feedback from you, we have two groups of users. Some users who could install Corra and ATAQS in Unix machines with IT support or computational biologists who have extended experience of Unix system. The other users, who often posted questions for installing questions, have no experience of installing any of required third party software stated in the installation guides (e.g., mysql, tomcat etc).
As a part of training, our newly joined group software engineer, Tommy Tran, created Virtual Images (VM) with me. The virtual images contain all of required software along with Corra and ATAQS. We recommend to use the Virtual image with minimum 2 GByte RAM (4 GByte RAM is preferable for small project) with minimum 20 GByte Hard Drive space. The two links (one for Corra and one for ATAQS) are in Seattle Proteome Center page
http://www.proteomecenter.org/software.php (click Download VM image).
This is not ideal setting for high through put with large dataset (especially for Corra application). For those users with high volume of dataset should really consider to put it as server applications with many computing nodes. However, the VM can serve in two ways: (1) for small dataset users, it's easy to just run the software (2) for IT, it can be served as template.
We send our best wish for your proteomics researches using label free quantification and SRM based verification study.
Warm Regards,
Mi-Youn Brusniak
--
Mi-Youn Brusniak, PhD
Computational Biologist/Sr. Software Engineer
Mi-Youn....@systemsbiology.org
p 206.732.1327
Institute for Systems Biology | Seattle Proteome Center | 401 Terry Ave N. Seattle WA 98109
Fabian Bindel
Nov 6, 2011, 5:57:00 AM11/6/11
to Corra
Dear Mi-Youn Brusniak,
I was so happy to read that you created a virtual machine in order
that user
can test easily your developed ATAQS. I thank you very much.
I immendiately downloaded it after I got the information mail from
google-groups.
I downloaded also VirtualBox for Windows. My machine is a Windows 7
64bit system (engl.).
But unfortunately I encountered a problem.
There was no problem the start the saved state of the virtual machine
but I was not able to do anything
inside the virtual machine. There was no mouse or keyboard
integration. Virtual Box
asked me if it should capture my mouse and I agreed but I was not able
to move the
other mouse pointer which is close to the address bar in firefox or
type anything.
So I read your recommendation for the settings for the virtual image.
Then I thought this might be the problem. But in order to change the
settings I had to
shutdown the virtual machine, thus loosing the saved state. I changed
to the
recommended settings (Base memory was at 768 MB and I increased the
video memory
from 12 to 128 MB). The gigabyte for the harddisk I did not change.
I started then the virtual machine again but then I was not able to
log into the system
because I have no information about the user login and password. But
the mouse and
the keyboard worked.
Since I thought I had only a problem with the mouse and keyboard
integration I switch
to another operating system MacOS X (10.6.8). Downloaded VirtualBox
and ATAQS and
started the virtual machine in the saved state as before. But there
was the same problem
of a "frozen" mouse pointer. Before I also was asked by VirtualBox if
I want to capture the
host mouse and I agreed, for sure.
Next I tried to open only the vmdk file in VMWare workstation Ver. 7
on my machine as a
new virtual machine but since I cannot transfer the saved state I
started their the operating
system. But then I was again not able to log in.
I google a bit for the problem about mouse integration into virtual
box and I found some
driver issues, etc. But there in all cases the user were able to
change the settings for the
virtual box and restart. Thus do you mind giving the people access to
the system (login name
& password)? Or do you have by any change an idea what the problem is
about no mouse
and keyboard integration and how I can change that?
@all: Are there any other users having the same problem? Do you mind
to share
your experience?
I am sorry for any inconveniences and I hope I am not too pushy with
this.
Thank you very much for all the effort you do for all the users out
there!!
I totally appreciate it.
Thank you very much and yours sincerely,
Fabian Bindel
On 1 Nov., 00:06, "Mi-Youn Brusniak" <mbrusn...@systemsbiology.org>
wrote:
>
> Computational Biologist/Sr. Software Engineer
> Mi-Youn.Brusn...@systemsbiology.org <mailto:mbrusn...@systemsbiology.org>
> p 206.732.1327
> Institute for Systems Biology <http://www.systemsbiology.org/> | Seattle
> Proteome Center <http://www.proteomecenter.org/> | 401 Terry Ave N. Seattle
> WA 98109
I was so happy to read that you created a virtual machine in order
that user
can test easily your developed ATAQS. I thank you very much.
I immendiately downloaded it after I got the information mail from
google-groups.
I downloaded also VirtualBox for Windows. My machine is a Windows 7
64bit system (engl.).
But unfortunately I encountered a problem.
There was no problem the start the saved state of the virtual machine
but I was not able to do anything
inside the virtual machine. There was no mouse or keyboard
integration. Virtual Box
asked me if it should capture my mouse and I agreed but I was not able
to move the
other mouse pointer which is close to the address bar in firefox or
type anything.
So I read your recommendation for the settings for the virtual image.
Then I thought this might be the problem. But in order to change the
settings I had to
shutdown the virtual machine, thus loosing the saved state. I changed
to the
recommended settings (Base memory was at 768 MB and I increased the
video memory
from 12 to 128 MB). The gigabyte for the harddisk I did not change.
I started then the virtual machine again but then I was not able to
log into the system
because I have no information about the user login and password. But
the mouse and
the keyboard worked.
Since I thought I had only a problem with the mouse and keyboard
integration I switch
to another operating system MacOS X (10.6.8). Downloaded VirtualBox
and ATAQS and
started the virtual machine in the saved state as before. But there
was the same problem
of a "frozen" mouse pointer. Before I also was asked by VirtualBox if
I want to capture the
host mouse and I agreed, for sure.
Next I tried to open only the vmdk file in VMWare workstation Ver. 7
on my machine as a
new virtual machine but since I cannot transfer the saved state I
started their the operating
system. But then I was again not able to log in.
I google a bit for the problem about mouse integration into virtual
box and I found some
driver issues, etc. But there in all cases the user were able to
change the settings for the
virtual box and restart. Thus do you mind giving the people access to
the system (login name
& password)? Or do you have by any change an idea what the problem is
about no mouse
and keyboard integration and how I can change that?
@all: Are there any other users having the same problem? Do you mind
to share
your experience?
I am sorry for any inconveniences and I hope I am not too pushy with
this.
Thank you very much for all the effort you do for all the users out
there!!
I totally appreciate it.
Thank you very much and yours sincerely,
Fabian Bindel
On 1 Nov., 00:06, "Mi-Youn Brusniak" <mbrusn...@systemsbiology.org>
wrote:
> Dear Corra and ATAQS Users,
>
> Based on feedback from you, we have two groups of users. Some users who
> could install Corra and ATAQS in Unix machines with IT support or
> computational biologists who have extended experience of Unix system. The
> other users, who often posted questions for installing questions, have no
> experience of installing any of required third party software stated in the
> installation guides (e.g., mysql, tomcat etc).
>
> As a part of training, our newly joined group software engineer, Tommy Tran,
> created Virtual Images (VM) with me. The virtual images contain all of
> required software along with Corra and ATAQS. We recommend to use the
> Virtual image with minimum 2 GByte RAM (4 GByte RAM is preferable for small
> project) with minimum 20 GByte Hard Drive space. The two links (one for
> Corra and one for ATAQS) are in Seattle Proteome Center pagehttp://www.proteomecenter.org/software.php(click Download VM image).
>
> Based on feedback from you, we have two groups of users. Some users who
> could install Corra and ATAQS in Unix machines with IT support or
> computational biologists who have extended experience of Unix system. The
> other users, who often posted questions for installing questions, have no
> experience of installing any of required third party software stated in the
> installation guides (e.g., mysql, tomcat etc).
>
> As a part of training, our newly joined group software engineer, Tommy Tran,
> created Virtual Images (VM) with me. The virtual images contain all of
> required software along with Corra and ATAQS. We recommend to use the
> Virtual image with minimum 2 GByte RAM (4 GByte RAM is preferable for small
> project) with minimum 20 GByte Hard Drive space. The two links (one for
>
> This is not ideal setting for high through put with large dataset
> (especially for Corra application). For those users with high volume of
> dataset should really consider to put it as server applications with many
> computing nodes. However, the VM can serve in two ways: (1) for small
> dataset users, it's easy to just run the software (2) for IT, it can be
> served as template.
>
> We send our best wish for your proteomics researches using label free
> quantification and SRM based verification study.
>
> Warm Regards,
>
> Mi-Youn Brusniak
> --
> Mi-Youn Brusniak, PhD
> <http://www.systemsbiology.org/Senior_Research_Scientists/Mi-Youn_Brus...>
> This is not ideal setting for high through put with large dataset
> (especially for Corra application). For those users with high volume of
> dataset should really consider to put it as server applications with many
> computing nodes. However, the VM can serve in two ways: (1) for small
> dataset users, it's easy to just run the software (2) for IT, it can be
> served as template.
>
> We send our best wish for your proteomics researches using label free
> quantification and SRM based verification study.
>
> Warm Regards,
>
> Mi-Youn Brusniak
> --
> Mi-Youn Brusniak, PhD
>
> Computational Biologist/Sr. Software Engineer
> Mi-Youn.Brusn...@systemsbiology.org <mailto:mbrusn...@systemsbiology.org>
> p 206.732.1327
> Institute for Systems Biology <http://www.systemsbiology.org/> | Seattle
> Proteome Center <http://www.proteomecenter.org/> | 401 Terry Ave N. Seattle
> WA 98109
Tommy Tran
Nov 7, 2011, 5:55:29 PM11/7/11
to Corra
Hi Fabian,
It seems like the keyboard/mouse issue is hardware dependent and will
vary base on your hardware. I have been using VirtualBox on two
different machines running Windows 7 natively and had no problems at
all with one but I had the same issue as you with the other. I fixed
it by installing the VirtualBox Extension Pack at https://www.virtualbox.org/wiki/Downloads
and adding my usb keyboard/mouse in the settings in VirtualBox.
The login and password are:
Username for ATAQS: ATAQSUser
Username for Corra: CorraUser
Password for both: password
Root password for both: password
These credential will work for both the CentOS login and the
application(ATAQS/Corra).
Thank you so much for trying out our VM Images and letting us know
about the missing credentials and I apologize for not putting those in
a readme/installation instruction earlier. I hope that helped and
please feel free to ask any additional questions you may have.
Regards,
Tommy Tran
> > Corra and one for ATAQS) are in Seattle Proteome Center pagehttp://www.proteomecenter.org/software.php(clickDownload VM image).
It seems like the keyboard/mouse issue is hardware dependent and will
vary base on your hardware. I have been using VirtualBox on two
different machines running Windows 7 natively and had no problems at
all with one but I had the same issue as you with the other. I fixed
it by installing the VirtualBox Extension Pack at https://www.virtualbox.org/wiki/Downloads
and adding my usb keyboard/mouse in the settings in VirtualBox.
The login and password are:
Username for ATAQS: ATAQSUser
Username for Corra: CorraUser
Password for both: password
Root password for both: password
These credential will work for both the CentOS login and the
application(ATAQS/Corra).
Thank you so much for trying out our VM Images and letting us know
about the missing credentials and I apologize for not putting those in
a readme/installation instruction earlier. I hope that helped and
please feel free to ask any additional questions you may have.
Regards,
Tommy Tran
Fabian Bindel
Nov 10, 2011, 10:51:02 AM11/10/11
to Corra
Dear Tommy Tran,
thank you very very much for the quick repsone and everything
works fine regarding the virtual machine, now. I was able to log in
and use mouse/keyboard after I restarted the virtual machine and
changed to the recommended settings. I logged in as ATAQSUser
and wanted to try ATAQS in Firefox but first I had to start the apache
server again via the terminal. Finally I got the login screen for
ATAQS
at localhost:8080/ATAQSTest/#login
As you mentioned the username and password is the same.
I tried to log in but I always get the message that the password or
username is invalid.
I tried both you mentioned and I tried the login data from the ATAQS
Demo Manual, too.
I thought this might be due to a not running database. Thus I tried to
start
mysql but I am not sure if I found the right commands for it in the
terminal.
I went to the home directory of the ATAQSUser and then to mysql/bin
and run the command "mysql start". But then I get the error message
Error 2002 (HYOO): Can't connect to lovcal MySQL server through socket
'/var/lib/mysql/.sock' (111).
I thought this might the the wrong directory to start MySQL from so I
tried it also from the etc/init.d and etc/rd.0 (this both I found via
google).
But the same error message occured.
Thus which (potentially other) services needs to be run? And how do I
start them.
I am really looking forward to test ATAQS!
Best Regards,
Fabian
On 7 Nov., 23:55, Tommy Tran <tran.t.to...@gmail.com> wrote:
> Hi Fabian,
>
> It seems like the keyboard/mouse issue is hardware dependent and will
> vary base on your hardware. I have been using VirtualBox on two
> different machines running Windows 7 natively and had no problems at
> all with one but I had the same issue as you with the other. I fixed
> it by installing the VirtualBox Extension Pack athttps://www.virtualbox.org/wiki/Downloads
> > > Corra and one for ATAQS) are in Seattle Proteome Center pagehttp://www.proteomecenter.org/software.php(clickDownloadVM image).
thank you very very much for the quick repsone and everything
works fine regarding the virtual machine, now. I was able to log in
and use mouse/keyboard after I restarted the virtual machine and
changed to the recommended settings. I logged in as ATAQSUser
and wanted to try ATAQS in Firefox but first I had to start the apache
server again via the terminal. Finally I got the login screen for
ATAQS
at localhost:8080/ATAQSTest/#login
As you mentioned the username and password is the same.
I tried to log in but I always get the message that the password or
username is invalid.
I tried both you mentioned and I tried the login data from the ATAQS
Demo Manual, too.
I thought this might be due to a not running database. Thus I tried to
start
mysql but I am not sure if I found the right commands for it in the
terminal.
I went to the home directory of the ATAQSUser and then to mysql/bin
and run the command "mysql start". But then I get the error message
Error 2002 (HYOO): Can't connect to lovcal MySQL server through socket
'/var/lib/mysql/.sock' (111).
I thought this might the the wrong directory to start MySQL from so I
tried it also from the etc/init.d and etc/rd.0 (this both I found via
google).
But the same error message occured.
Thus which (potentially other) services needs to be run? And how do I
start them.
I am really looking forward to test ATAQS!
Best Regards,
Fabian
On 7 Nov., 23:55, Tommy Tran <tran.t.to...@gmail.com> wrote:
> Hi Fabian,
>
> It seems like the keyboard/mouse issue is hardware dependent and will
> vary base on your hardware. I have been using VirtualBox on two
> different machines running Windows 7 natively and had no problems at
> all with one but I had the same issue as you with the other. I fixed
>
> > > This is not ideal setting for high through put with large dataset
> > > (especially for Corra application). For those users with high volume of
> > > dataset should really consider to put it as server applications with many
> > > computing nodes. However, the VM can serve in two ways: (1) for small
> > > dataset users, it's easy to just run the software (2) for IT, it can be
> > > served as template.
>
> > > We send our best wish for your proteomics researches using label free
> > > quantification and SRM based verification study.
>
> > > Warm Regards,
>
> > > Mi-Youn Brusniak
> > > --
> > > Mi-Youn Brusniak, PhD
> > > <http://www.systemsbiology.org/Senior_Research_Scientists/Mi-Youn_Brus...>
>
> > > Computational Biologist/Sr. Software Engineer
> > > Mi-Youn.Brusn...@systemsbiology.org <mailto:mbrusn...@systemsbiology.org>
> > > p206.732.1327begin_of_the_skype_highlighting 206.732.1327 end_of_the_skype_highlighting
> > > This is not ideal setting for high through put with large dataset
> > > (especially for Corra application). For those users with high volume of
> > > dataset should really consider to put it as server applications with many
> > > computing nodes. However, the VM can serve in two ways: (1) for small
> > > dataset users, it's easy to just run the software (2) for IT, it can be
> > > served as template.
>
> > > We send our best wish for your proteomics researches using label free
> > > quantification and SRM based verification study.
>
> > > Warm Regards,
>
> > > Mi-Youn Brusniak
> > > --
> > > Mi-Youn Brusniak, PhD
> > > <http://www.systemsbiology.org/Senior_Research_Scientists/Mi-Youn_Brus...>
>
> > > Computational Biologist/Sr. Software Engineer
> > > Mi-Youn.Brusn...@systemsbiology.org <mailto:mbrusn...@systemsbiology.org>
Tommy Tran
Nov 10, 2011, 3:32:13 PM11/10/11
to Corra
Hi Fabian,
When starting up the tomcat server make sure you are running as the
'tomcat' user. The password for tomcat is also 'password' and the
scripts are in /home/tomcat/apache-tomcat-6.0.32/bin. Once you have
that started you can start up mysql by running this command as root:
/usr/bin/mysqld_safe &
Alternatively you can have mysql running on startup by running this
command as root:
/sbin/chkconfig mysqld on
Thank you again for trying out the ATAQS VM image.
Regards,
Tommy Tran
On Nov 10, 7:51 am, Fabian Bindel <bindel.fab...@googlemail.com>
When starting up the tomcat server make sure you are running as the
'tomcat' user. The password for tomcat is also 'password' and the
scripts are in /home/tomcat/apache-tomcat-6.0.32/bin. Once you have
that started you can start up mysql by running this command as root:
/usr/bin/mysqld_safe &
Alternatively you can have mysql running on startup by running this
command as root:
/sbin/chkconfig mysqld on
Thank you again for trying out the ATAQS VM image.
Regards,
Tommy Tran
On Nov 10, 7:51 am, Fabian Bindel <bindel.fab...@googlemail.com>
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