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Application Software

Basic description of the application software, installed/wanted on the WindCompS

Application Software on the WindCompS

The following software in installed on (at least one of) the BIMSB-WCS-xx Computers: Xcalibur, Proteome DiscovererMaxQuantChromaTOFMascot-ClientReAdWProteoWizardR

If you feel demand for further software or Windows-tools, please address to the BIMSB-Bioinformatics-Administrators (Dan Munteanu Ricardo Wurmus) or David Arnold or Martin R. Siegert. While working remote without easy access to you E-Mail client, you also could use the built-in messaging tool of plone/BBC to contact Martin.

 

Please also read the other pages on Server-Design (Hardware, IP-Address, current status) and Accessing (via Remote Desktop) WindCompS.

 

Application Matrix

 "X" = Installed Application; "+" = Installed Component/Tool; "o" = Could be installed on demand

"-" = Not installed; "--" = incompatible to install; "::" = No installed because of broken depencency

BIMSB-WCS-xx 01 02 03 04 05 06 07 (08) 09  BIMSB-WS01
 Highlight
(01-04=PM, 05-09=VM)
4core 4core 4core 4core
64bit
3GHz 3GHz 3GHz
64bit

IPAR
64bit
nUser
64bit 
Xcalibur
- Thermo Foundation 1.0
- Xcalibur 2.1
- TF Program
MSFileReader (v2.2)
X
+
+
+
2.2
X
+
+
+
2.2
X
+
+
+
o
--
--
::
::
2.2
X
+
+
+
2.2
 



2.2
--
--
::
::
o

--
--
::
::
2.2
--
--
::
::
2.2
Proteome Discoverer (SEQUEST)
- License (- = Viewer only)
- InforSense VM
X
+
+
X
-
o
X
-
o
--  X
-
o
  --
--   --
Pinpoint 1.1 - X - - -   -   - -
ReAdW X X X ::    ::
:: ::
ProteoWizard
- v1.6.0
- v3.0.3476
X
-
X
-
X
-
:: X
-
  ::
:: X
X
MaxQuant
- Installed v-1.0.13.13
- Installed v-1.1.0.0
- Installed v-1.1.1.25
- Installed v-1.2.2.5

X
X
-
o

-
-
-
X

X
X
-
o
 
--
-
-
X

-
-
-
X
 
-
-
-
X

--
X
-
X


--
-
-
X

--
X
-
o
Mascot Daemon (Client)  X X  -- X   -
-
Mascot Server - - - - - - -
- X
ChromaTOF (dongled)        planed            
Illumina Genome Studio
Sequencing Analysis Viewer
X
X
X
X
X
X
X
X
X
X
X
X
X
X

X
X
::
R (Statistics)     X X         X  
Java Runtime JRE 7u45 7u45 7u45 7u45 7u45 7u45 7u45   7u45 X
Microsoft .NET Framework
- 1.1
- 2.0 SP2
- 3.0 SP2
- 3.5 SP1
- 4 Client Profile
- 4 Extended

x
x
x
x
x
x

x
x
x
x
x
x
 





x


x
x
x
x
x







x
x
x
x
x
x


x
x
x
x
x
 

x
x
x
x
x




x
x

Visual C++ 2008 Redist. 9.0
Visual C++ 2010 Redist. 10.0
X
X
X

X
X
  X
X
X
X
X
X
  X
X
 
Adobe Reader v11.0.8.4 X X X X older X X
X X
Adobe Flash Player v16.0.0.305 X X X X older X X
X -
MS-Office              
  planed
Open-Office v3.3.0 X X X X X X X
X X
Lab-Management Tools              
  planed
WinSCP v4.2.5 X X X X X X X
X X
CygWin           X      
HxD Hex Editor v1.7.7.0                  
raw-2-mzML converter - - - - - - - - - X
                     

Details on each installed Software

Illumina Genome Studio

Data-Visualisation (and Analysation) for Illumina Sequencing data (SNPs et ct.)

http://www.illumina.com/software/genomestudio_software.ilmn

  • Requested by: Sebastian Froehler
  • Scientiftic 1st Level Support: Giannino Patone
  • License: Installed on WCS-09 (while still being iPAR server, prior to P2V-Migration)
  • Version: 2008 (all 1.0.x modules) -or- 2011.1 (Viewer v1.9.0 module only)
  • Requires: Microsoft .NET Framework 3.5 (Notice: ".NET 4" is not accepted)
  • Installed on: BIMSB-WCS-01 tru 07 (viewer), BIMSB-WCS-09 (full, old v2008), BIMSB-WCS-02 (full, current v2011.1)
  • Database "dbSNP 130" (3GB) is installed on WCS-01 tru -04 (physical machines) only.

 

Illumina Sequencing Analysis Viewer

Real-time verification of Illumina Sequencing quality metrics.

http://www.illumina.com/support/sequencing/sequencing_software/sequencing_analysis_viewer_sav.ilmn

  • Requested by: Sebastian Froehler
  • Scientific 1st Level Support: Sebastian Froehler
  • Manual: Available here
  • License: Covered by HiSeq Hardware users.
  • Version: 1.8.40
  • Requires: Microsoft .NET Framework 4.0 "Extended" (the "4.0 Client Profile" is not sufficient)
  • Installed on: BIMSB-WCS-01 tru 09

 

MaxQuant

Quantitative proteomics software package for analyzing large (high-res.) mass spectroscopy datasets.

http://www.maxquant.org/

  • Requested by: Guido M.
  • Scientific 1st Level Support: Guido M.
  • License: Freeware
  • Version 1.0.13.13 (32bit) (up to now: unofficial Developer-Version with extra features, but not to be spread to the broad public --> Special-group to ACL Devel.exe)
    • Requires: Xcalibur, Mascot-Client v2.2 and current mascot.dat matching the one on the Server (WS01).
    • Installed on BIMSB-WCS-01, -02, -03 and -05
    • Removed on BIMSB-WCS-02, -05 in May 2012
  • Version 1.1.0.0
    • does not depend on 32bit-Xcalibur
    • Installed on BIMSB-WCS-01 tru -05 and -07 and WS01 (but no configured yet!!)
    • Removed on BIMSB-WCS-02, -04, -05 in May 2012
  • Version 1.1.1.25
    • Requires: MS-FileReader v2.1 (available for 64bit too), Microsoft .NET 4 Framework
    • Installed on BIMSB-WCS-04 
    • Removed on BIMSB-WCS-04 in May 2012
  • Version 1.2.2.5
    • Requires: MS-FileReader v2.2, Microsoft .NET 4 Framework, VisualC++ 2008 and 2010 Redistributables
    • Installed on: BIMSB-WCS-02, -04, -05, -06, -09

ChromaTOF

Analysis-Software for GC_GC_TOF-MS results

http://www.leco.com/products/sep_sci/chromaTOF/chromaTOF.htm

  • Requested by:
  • Scientific 1st Level Support: N.N.
  • License:
  • Version: 4.20
  • Requires:
  • Installed on BIMSB-WCS-nn

Mascot-Daemon (Client)

Access (search) mass spectroscopy database, containing peptide mass fingerprints of enzymatic digest of protein.

http://www.matrixscience.com/search_intro.html

  • Requested by: Guido M.
  • Scientific 1st Level Support: Guido M.
  • License: Matrix Science Inc (Daemon is free); Server to be installed on WS-2k8-64bit, License requested)
  • Version: 2.2.2 (32bit)
  • Requires: Contact to Selbach-group (existing server, sometimes too slow administered)
  • Installed on: BIMSB-WCS-01, -02, -03 and -05

ReAdW

Tool for Xcalibur, to convert .RAW to .mzXML

http://tools.proteomecenter.org/wiki/index.php?title=Software:ReAdW

  • Requested by: Dominic Tolle
  • Scientific 1st Level Support: Dominic Tolle
  • License: N.N.
  • Version: 4.3.1 (32bit)
  • Requires: Xcalibur (XRawfile Library) by ThermoFinnigan
  • Installed on: BIMSB-WCS-01, -02, -03 and -05 (Copy 2 files to C:\Xcalibur\system\programs, which is in the PATH after Thermo-install)

 

Pinpoint

Rapid Biomarker Verification

http://www.thermoscientific.com/pinpoint

  • Requested By: Fabian Bindel
  • Scientific 1st Level Support: Fabian Bindel
  • License: 1 License for Stefan Kempa, used on WCS-02
  • Version: 1.1 (32bit)
  • Requires: .NET Framework 3.5 SP1
  • Installed on: BIMSB-WCS-02

ProteoWizard

Tools and software libraries for proteomics data analysis.

http://proteowizard.sourceforge.net

  • Requested by: Dominic Tolle
  • Scientific 1st Level Support: Dominic Tolle
  • License: OpenSource (Apache v2)
  • Version: 1.6.0 (32bit), on WS01 also 3.0.3476 (64bit, Apr. 2012)
  • Requires: Xcalibur (XRawfile Library) by ThermoFinnigan or "MSFileReader" (see MaxQuant 1.1.1)
  • Requires: some MS Visual-C libraries (also part of Xcalibur)
  • Installed on: BIMSB-WCS-01, -02, -03 and -05 (Copy all 50 files [excluding the additional "50 hidden" ones for MacOS] to C:\Xcalibur\system\programs, which is in the PATH after Thermo-install)
  •  

Proteome Discoverer

Tool for Xcalibur, to ...

http://N.N.

  • Requested by: Guido M.
  • Scientific 1st Level Support: Guido M.
  • License: The (one) purchased license (based on hostid) is installed on BIMSB_WCS-01. On all other WindCompS a 30-days demo-license was activated upon install (only valid for VNC, not RDP!), valid until December 2009; afterwards the other WindCompS serve as "Viewer" only.
  • Version:1.0.0.43 with SP1 (32-bit)
  • Requires: Xcalibur 2.1 (XRawfile Library) by ThermoFinnigan, Microsoft .NET Framework 3.5
  • Installed on: BIMSB-WCS-01, -02, -03 and -05

 

R

Script-language and environment for statistical computing and graphics

http://www.r-project.org/

  • Requested by: Markus Wenzel
  • Scientific 1st Level Support: Markus Wenzel
  • License: free (GNU GPL)
  • Version: 2.10.0 (32- and 64-bit)
  • Requires: nothing
  • Installed on: BIMSB-WCS-03, -04 and -09

 

raw-2-mzML converter

Custom made automatic file conversion service by Martin Siegert (using msconvert from Proteo Wizard, see above)

  • Requested by: Dominic Tolle
  • Scientific 1st Level Support: none (Martin Siegert for Technical issues)
  • License: free
  • Version: July 2011
  • Requires: Proteo Wizard, subinacl.exe (from WS2k3-Tools)
  • Installed on: \\BIMSB-WS01\WCS-Data\CF_Dieterich\raw2mzML

 

Xcalibur

Data analysis software for Thermo Scientific mass spectroscopy and related instruments.

http://www.thermo.com/com/cda/product/detail/1,1055,1000001009250,00.html

  • Requested by: Stefan Kempa
  • Scientific 1st Level Support: N.N.
  • License: Part of Measuring-Instruments
  • Version: 2.1.0 build 1139 (32bit)
  • Requires: Microsoft .NET Framework 3.5 (Notice: ".NET 4" is not accepted)
  • Requires: Thermo-Platform (--> MSMQ-Windows-Component), which does not install on 32bit!
  • Includes/Provides: Thermo-Platform ("Foundation" v.1.0.0.42), FT-Programs (v.2.1.0.40)
  • Installed on BIMSB-WCS-01, -02, -03 and -05

 

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