Software download of the Institut für Klinische Molekularbiologie

MFG Tools

The MFG Tools package includes GenoTool, PatientTool and SampleTool.

Download Executables

These tools are available as executables. Just unpack them and install them on your client machine.

These packages include a script called 'CreateDatabase.sql'. Run this script on your MSSQL server and it will create all the tables, dependancies, and stored procedures that you need.

MFG Executables (13.7 MB, zipped, Windows 95/98/NT)
MFG Executables (13.7 MB, self-extracting, Windows 95/98/NT)


Download Source Code

We have provided the source code for these tools for download as well. For normal use, you will not need the source code, only if you want to take the tools apart and see how they work.

We used two commercial packages to make these tools, True DBgrid 6.0 and Olectra Chart 6.0. Both are available from ComponentOne.

MFG Visual Basic Source Code (0.7 MB, zipped, Windows 95/98/NT)


Installation Tips and Tricks

You will need Microsoft Universal Data Access version 2.5 to make your data connections. The latest version of MDAC_typ.exe can be downloaded directly from Microsoft.
You will need to add the MSSQL servers IP address to your lmhosts file so your client can connect. Use the file finder to find the lmhosts file on your system, and read the instructions.

To use the MFG Client Tools, you must know:
the name of the database server,
the name of the database,
your database login name
and your password.

Ask the person who installed your database if you have questions.
In SampleTool use "control + mouse button" to drag samples onto the plate.
Sources cannot be added using the VB Clients, they must be added to the database using SQL statements. Contact your database administrator if you cannot do this yourself.
This software is not guaranteed to be bug free. Use at your own risk. But, we would be happy to hear from you if you find any problems with our software.


System Requirements

  • Database server running Microsoft SQL Server version 7.0
  • Client machine(s) running Windows NT 4, service pack 6a (Windows 9x/2000/XP should also work, but we have not tried them)
  • A TCP/IP connection between the server and the clients

 


When using please cite the following publication:
Hampe J, Wollstein A, Lu T, Frevel HJ, Will M, Manaster C, Schreiber S (2001).
An integrated system for high-throughput TaqMan ™ based SNP genotyping.
Bioinformatics 17: 654-655
PubMed (PMID:11448884)


LIMS Tools

The LIMS Tools package includes AssayManager, OrderTool and ProjectManager.

Download Executables

These tools are available as executables. Just unpack them and install them on your client machine.

LIMS Tools (36.5 MB, zipped)


Download Source Code

We provide the Visual Basic source code for these tools for download as well. For normal use, you will not need the source code, only if you want to take the tools apart and see how they work.

LIMS Tools Visual Basic Source Code (230 KB, zipped)


Installation Instructions

  • Run the LIMS_full_ddl.sql script in a newly created database on your SQL Server (version 7.0). You may wish to edit this script to add your own users
  • You may run the script LIMS_sampledata.sql to insert some sample data into the database
  • You can find help on how to use the programs in the included html help files (AssayManager, ProjectManager) or in the readme file (OrderTool)

 

System Requirements

  • Database server running Microsoft SQL Server version 7.0
  • Client machine(s) running Windows NT 4, service pack 6a (Windows 9x/2000/XP should also work, but we have not tried it)
  • Version 2.5 or higher of Microsoft Universal Data Access (MDAC)
  • A TCP/IP connection between the server and the clients

 


When using please cite the following publication:
Teuber M, Koch WA, Manaster C, Wächter S, Hampe J, Schreiber S (2005).
Improving quality control and workflow management in high-throughput single-nucleotide polymorphism genotyping environments.
JALA 10(1): 43-47
abstract


POPSIM

We have created a population simulation program POPSIM, that

  • creates a virtual representation of every individual,
  • makes no prior assumptions but the Medelian rules and
  • allows for populations of several million individuals size to be generated and to be followed over hundreds of generations.

 

The parameters of the disease model, population structure and population expansion rate can be specified. Flexible sampling options exist, that allow samples of families and individuals to be drawn at any given point during the population history. The program may be a useful tool in the study of the influence of genetic drift, recombination and admixture on the generation and maintenance of linkage disequilibrium in populations as well as the evaluation of stochastic sampling characteristics of families and individuals conditional on a complex genetic phenotype from homogeneous and heterogeneous populations.
Popsim is a command line driven program, that gets all it`s information from a command file.

download: POPSIM (71 KB, zipped)

sample command file: experiment.pop_init

sample output files:
Linkage file format: experiment.pop_lnk
Population overview: experiment.pop_ovw
Population overview Table-Fileformat: experiment.pop_ovw
Population progresslog: experiment.pop_pro

When using please cite the following publication:
Hampe J, Wienker T, Schreiber S, Nürnberg T (1998).
POPSIM: A general population simulation program.
Bioinformatics 14: 458-464
PubMed (PMID:9682059)


DRBTool

DRBTool supports a new technique for determining HLA genotypes at the DRB1 locus through non-electrophoretic scoring of group-specific PCR.

Two versions are available. The "DRBToolTextMode" version supports only construction of DRB1 genotype; the "DRBTool" supports this and also Mendel checking and database import.


DRBTool (3.1 MB, zipped), database (MS SQL Server 7.0) required

DRBToolTextMode (3.1 MB, zipped), no database required


These tools have been developed for Windows NT 4 service pack 6a.
Windows 2000/XP should also work, but we have not tried it.


When using please cite the following publication:
Hampe J, Valentonyte R, Manaster C, Teuber M, Jenisch S, Entz P, Nagy M, Schreiber S (2004).
Nonelectrophoretic method for high-throughput HLA-DRB1 group genotyping.
BioTechniques 36: 148-151
PubMed (PMID:14740497)


Entropy

Entropy is a PERL program that uses an EM algorithm for haplotype frequency estimation. It reads standard linkage format files.

Entropy (49 KB, zipped)

When using please cite the following publication:
Hampe J, Schreiber S, Krawczak M (2003).
Entropy-based SNP selection for genetic association studies.
Hum Genet 114(1): 36-43
PubMed (PMID:14505034)


SNPSelection

The power of a genome-wide disease association study depends critically upon the properties of the marker set used particularly the marker number, the physical spacing of markers, and the level of inter-marker association due to linkage disequilibrium. Extending the theoretical framework for the entropy-based selection of genetic markers, we have developed a local measure of the relative efficacy of a marker set, compared to including a maximally polymorphic SNP at the map position of interest. Based on this local measure we have implemented an algorithm to select the maximal informative set of markers from a given marker set.

SNPSelection Website

When using please cite the following publication:
Wollstein A, Herrmann A, Wittig M, Nothnagel M, Franke A, Nürnberg P, Schreiber S, Krawczak M, Hampe J (2007).
Efficacy assessment of SNP sets for genome-wide disease association studies.
Nucleic Acids Res 35(17): e113
PubMed (PMID:17726055)