It is the time of the year were the sourceforge.net votes are up for the best project of the year and we would highly appreciate it, if you would vote BinBase as the best project.

Please do this by pressing the link below and select the category: 'Best Project For Academia'

nominate for the best project of the year

thanks you,

gert wohlgemuth

It is the time of the year were the sourceforge.net votes are up for the best project of the year and we would highly appreciate it, if you would vote BinBase as the best project.

Please do this by pressing the link below and select the category: 'Best Project For Academia'

nominate for the best project of the year

thanks you,

gert wohlgemuth

BinBase 3.3 is released and the itanium architecture is not longer supported

hello

as you might notice we have now a new design for the webpage where we hope it's easier and better to understand than the old version.

 gert

we are currently working on the BinBase 3.1 version and provide a vmware server 2.0 image for this reason. This file give you the possiblity to test BinBase without any major installation or setup from your side and we highly recommend that you give it a try.

If you are interrested, please send me an email (Gert Wohlgemuth - wohlgemuth@ucdavis.edu) and I will provide with a link to this image. We will upload the image for your use as soon as we determine that the software is stable, but this can take a couple of days or weeks.

how to use the image:

• register it with your vmware server 2.0
• start the image
• edit /etc/hosts and modify the ip address the actual ip address of this host, we are working on a patch to avoid this step
• execute /etc/inet.d/jboss stop
• execute /etc/inet.d/jboss start
• go to the jmx console and adjust the value of the database server ip address to the actual ip address
• go to ip:8080/binbase-compound and look at the defined bins

features of the image:

• BinBase 3.1 RC 1
• predifined database "binbase" comes with 9 samples from the potato dataset
• password and username for all functions are binbase/binbase
• compatible to the latest bellerophon version

Bellerophon 1.0.4 released

• improved stability
• rudimentary support for volatile database queries, the related binabse version is not released yet and comes soon
• several possibilities to filter views after queries
• improved mass spec search which shows a progress of the search and is generally faster, depending on the used hardware (<3s on a mac pro, <30s on a T42 IBM Laptop to compare one bin against 10000 mass specs)
• possibility to highlight all bin's which are found in a registered library
• several other small things

download

we just would like to inform that this project is under active development and we are try to fix bugs as fast as possible. The only reason for no recent activity is that the single developer was in vacation and busy traveling around and had just no time.

We do hope to keep the timeline and release the next verion at the end of this month. This version is supposed to contain support for large massspecs and volatile data + standards for volatile databases.

regards,

gert

all binbase downloads are now handled over sourceforge. The reason for this is that people complained that the project seems to be so inactive or that it's so hard to find the download button. I hope this makes it easier to get BinBase. If you have questions please contact me under wohlgemuth@ucdavis.edu

DOWNLOAD

getting help is easy

if you need help please contact gert wohlgemuth - wohlgemuth at ucdavis dot edu or better send messages to the BinBase mailling list.

link to the BinBase mailing list

easier builds

A BinBase maven mirror is now available for easier builds. Basically we hold all the needed packages for a successful build in one place! It is already defined in the pom.xml and if you build now from the latest svn version you don't have to download and install any dependencies anymore.

 A direct url to the repository is: http://binbase.fiehnlab.ucdavis.edu:8081/artifactory/repo/

release - 1.0.2

we just released a new bellerophon version (1.0.2)

new features

• visualization of meta data using a graph API
• you don't have to be an admin to use it, normal users can access it now in read only mode

BinBase installer

the BinBase database installer is now available in form of the BinBase only version. We will provide the BinBase + setupx installer in a couple of days.

Cluster installer

we also release the cluster installer in case you are only interested in the cluster part of the BinBase and don't want to use the algorythms. 

Where can I find them

you can find both here 

status update

we are more or less done with the internal restructuring. The automated build system is still a little bit shaky, but overall everything works as before. We reduced the memory usage of the build system from 2GB of R.A.M to less than one except for the build of the installer.

rcp applications

the BinBase RCP applications are now available for download.

bellerophon

binbase runtime monitor

BinBase Repository

BinBase binaeries are now available in our maven2 snapshot repository.

binbase maven2 snapshot repository