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Welcome to Liebel-Lab @ KIT - Institute of Toxicology & Genetics

by Urban Liebel last modified 2008-08-29 15:13

We are interested in bridging biology, engineering and computer sciences. Our interdisciplinary labs combine expertise in the development of novel High Content Screening platforms (automated microscopes), assay development, Computer Aided Microscopy (image processing PC "replaces" human operator during night hours), micro-arrays (bio-molecules on glass slides), bioinformatic data integration ("Bioinformatic Harvester"), high throughput image analysis (millions of images need to be analysed in very short time), lab robotics , labview rapid prototyping and most importantly -> fun.

KIT Screening Center


  • See "products and services" for our expertise and services
  • See "collaborations list" for ongoing projects.
  • Post-doc: If you think about a 2-3 years post-doc position before you "go to industry",
    we can offer you a unique environment of bio-labs, methods, equipment, 24 institutes (~4000 people) and company-contacts...and most important: fun :-)

  • Master/Bachelor/Diploma thesis are available in the various disciplines.
    Please contact us: urban.liebel (at) kit (dot) edu

YACY Sciencenet Search engine (search ~175.000.000 scientific webpages)

yacy-network+ YaCy-Sciencenet is a distributed search engine prototype based on "peer2peer" technology (Michael Christen et al.).
+ Instead of copying the internet into a data-center (google approach), YaCy peers (PC+YaCy software) share data itself
+ Each YaCy-PCs communicates with a network of distributed peers only if data is queried.

Features of YaCY search engine software
:

+ Allows indexing/searching anything from small websites to global scale data repositories
+ Indexes text, images, docs, pdf, ppt etc (200 document types)
+ Holds up to 5 Mio webpages or documents per PC.
+ Allows netorks of 1000s of PCs
+ Requires no cooling racks (standard PCs)
+ Requires less power (compared to 1HE server units)

+ Try it: http://sciencenet.fzk.de

Sciencenet goal
: Independent and open search engine for scientific content.
Ideally every institute/University runs it´s own search peer (PC + YaCy software) and contributes to the network

Sciencenet status:

+ 44 low cost PCs + YaCy software
+ ~100.000.000 documents ~ 500.000.000 words indexed

Links: a) Sciencenet overview b) Connected sciencenet peers c) YaCy.net project page d) Full sciencenet article

  • KIT Screening Centre - building 341
KIT-screening-center-interdisciplinaryBuilding 341 is almost in the centre of the campus and an ideal place for projects, which require expertise from several disciplines and institutes.

Building 341 is now home for:

* Bioinformatic Harvester the bioinformatic meta search engine (1000s of scientists use it daily).

* YACY-Sciencenet a distributed search engine based on "peer2peer" technology

* Bioinformatic webservices

* Screening microscope developments

* Large scale Screening data analysis
* ASIC-Search a novel processor design for fast genome sequence searches
* Lab automation projects
* LabView developments
* Scientific instrument developments


  • Bioinformatic Harvester III at KIT (Karlsruhe Institute of Technology)...
bioinfo-databases"Bioinformatic Harvester III" is a one-stop portal for major protein/gene information resources. Currently > 28 database are integrated or cross-linked. A convenient search interface allows real-time data retrieval.

* Searching and cross- linking major bioinformatic resources
* Fast meta search engine
* Harvesting human, mouse, rat, zebrafish, arabidopsis and drosophila information.

...find Harvester III here : http://harvester.fzk.de

See the Harvester article for details




  • High Content Screening facility at KIT (Karlsruhe Institute of Technology)
Scan^R microscope (collaboration with Olympus Europa and Olympus Soft Imaging Solutions). We developed the Scan^R Screening station software in collaboration with Olympus. The machines can be found in many labs already and allow fully automated high quality image acquisition. The KIT screening facility offers several Scan^R screening devices (latest generation), data storage solutions and an image processing cluster.

We use the Labview (National Instruments) based Scan^R software not only for routine screens, but also for novel technology development and integration (robotics, optic device control, detectors, specimen handling etc).
Features of the Scan^R which are of major importance:
* MT20 ultra stable Xe light source.
(Image processing software favours continues image quality)
* Scan^R real-time controller device for precise and stable device control.
* Cell detecting autofocus. Biological specimen often contain cells in different states of cell phase and therefore have different shapes and heights . The Autofocus allows to detect and focus on the cells of interest.

.

  • Development of a fast sequence pattern search device (ASIC-Vespa) - (Avi Esptein, Eduard Gursky)

    asic-vespaThe search engine board allows fast, genome-wide sequence based searches.
    See the Bioinformatic Harvester "Sequence search" for a DEMO. It complements traditional text based search engines.
* Figure: Custom search engine board with up to 16 GByte memory (right)
* Bottom left: Four "ASIC CPUs" with 4x 1000 processor units each.
* Center: FPGA for data handling.

Info: For Sequence search application the "ASIC CPUs" is at least 250x faster than a conventional "PC CPU".

Currently we use 4 ASICS/board.
Planned: 4-32 ASICS/board (= 32 x 1000 processing elements)


  • 2006-present: Development of CAM (computer aided microscopy) and the "MatrixScan" software
    (Collaboration with Leica Microsystems - Frank Sieckmann - Michael Held)

    Leica SP5"Matrix-Scan" is a software interface that allows remote control of Leica SP5 confocal microscopes.
    (see the Leica website for further information)

    Example (low level) application:
    1.utomatically pre-scan one or several slides (by means of the cell based autofocus):
    2.use the "click-tool" to select tens or hundreds of cells of interests from the gallery
    3.the microscope scans the selected cells at ultra high resolution in batch mode (over night/ weekend).

Example (high level) application: LabView software interface for online image processing.
We have developed LabView software modules that analyse images during the scan. You can use the LabView image processing routines e.g. to detect certain cell types. Once a certain cell type has been detected, the LabView software (running on a separate computer) "tells" the microscope to load a pre-defined high resolution IPS (higher magnification, more colors, water objective, laser intensitiy) for a certain amount of time. Any function of the SP5 can be changed automatically via the LabView remote control based on the image processing. After a cell of interest has been imaged, the SP5 microscope switches back to "normal" and continues searching at low resolution. Please find details in the Leica article...

Interesting Labview links: >> "LIBSVM Support Vector machines" developed by Chang and Lin >> National instruments support website >> VI package manager developed by Jim Kring.


  • old lab: 2004-2006: “Mitocheck-project-team” , EMBL Heidelberg, Olympus collaboration
    High speed time lapse microscopy for genome wide siRNA screens - 177.000 movies, ~15.000.000 images, 42 TByte of raw image data) read more

    mitocheck banner

We developed a novel live cell High-Content-Screening platform for the Mitocheck project in collaboration with Olympus. The platform consists of three parallel running Scan^R microscopes. Each microscopes images 4 LabTek Chamber slides with a total of 1536 siRNA experiments on it over 48 hours. A genome-wide gene-knockdown has been performed with a data set as large as 15.000.000 images and ~177. 000 cell division movies. See mitocheck.org (@ Sanger Institute for details)

MitoCheck is an integrated research project which brings together leading European research groups to study systematically the regulation of mitosis in human cells.MitoCheck is co-ordinated by Dr Jan-Michael Peters from the Institute of Molecular Pathology (IMP) in Vienna. The project aims to test all human genes for involvement in mitosis by RNAi, then identify a subset which will be studied intensively for changes in phosphorylation, subcellular localization and involvement in protein complexes. Other aspects will look at engineering mitotic kinases and translational opportunities for human health.


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