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Welcome to Liebel-Lab @ KIT - Institute of Toxicology & Genetics
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.
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YACY Sciencenet Search engine (search ~175.000.000 scientific webpages)  + 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 |
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 Building 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 |
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 "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 |
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 (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. |
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* 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) |
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Example (high level) application:
LabView software interface for online image processing. |
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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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The search engine board allows fast, genome-wide
sequence based searches.
"Matrix-Scan" is a software interface that allows
remote control of Leica SP5 confocal microscopes.
Sciencenet Search engine based on YACY p2p technology ...upgraded