www.jakubpas.net

GRDB – Gene Relational DataBase

2011-11-10T13:32:00.001+01:00

We have developed a fully automated web service available for the academic community which purpose is to increase the sensitivity of the detection of distantly related protein families. Predicted secondary structure information was added to the information about sequence conservation and variability, a technique known from hybrid threading approaches. The accuracy of the meta proﬁles created this way is compared with proﬁles containing only sequence information and with the standard approach of aligning a single sequence with a proﬁle. Additionally, the alignment of meta proﬁles is more sensitive in detecting remote homology between protein families and more effective than aligning two sequence-only proﬁles or proﬁle to sequence. The speciﬁcity of the alignment score is improved in it’s lower range compared to the robust sequence-only proﬁles. (More)

NaRCiSuS

2010-10-18T18:00:00.000+02:00

Structural genomics is the wide term which describes process of determination of structure representation of information in human genome and at present is limited almost exclusively on proteins. Although in common understanding genetic information means “genes and their encoded protein products”, thousands of human genes produce transcripts which are important in biological point of view but they do not necessarily produce proteins. Furthermore, even though the sequence of the human DNA is known by now, the meaning of the most of the sequences still remains unknown. It is very likely that a large amount of genes has been highly underestimated, mainly because the actual gene finders only work well for large, highly expressed, evolutionary conserved protein-coding genes. Most of those genome elements encode for RNA from which transfer and ribosomal RNAs are the classical examples. But beside these well-known molecules there is a vast unknown world of tiny RNAs that might play a crucial role in a number of cellular processes. Those elements are named Noncoding RNAs (ncRNA) and they perform their function without transcription to the protein product.
Here is proposed development of integrated bioinformatics platform that is specifically addressed for detecting, verifying, and classifying of noncoding RNAs. This complex approach to "Computational RNomics" will provide the pipeline which will be capable of detecting RNA motifs with low sequence conservation. It will also integrate RNA motif prediction which should significantly improve the quality of the RNA homolog search.

PEOPLE-RG-2009-249211

ELM: the status of the 2010 eukaryotic linear motif resource

2010-01-01T12:29:00.000+01:00

Linear motifs are short segments of multidomain proteins that provide regulatory functions independently of protein tertiary structure. Much of intracellular signalling passes through protein modifications at linear motifs. Many thousands of linear motif instances, most notably phosphorylation sites, have now been reported. Although clearly very abundant, linear motifs are difficult to predict de novo in protein sequences due to the difficulty of obtaining robust statistical assessments. The ELM resource at http://elm.eu.org/ provides an expanding knowledge base, currently covering 146 known motifs, with annotation that includes >1300 experimentally reported instances. ELM is also an exploratory tool for suggesting new candidates of known linear motifs in proteins of interest. Information about protein domains, protein structure and native disorder, cellular and taxonomic contexts is used to reduce or deprecate false positive matches. Results are graphically displayed in a 'Bar Code' format, which also displays known instances from homologous proteins through a novel 'Instance Mapper' protocol based on PHI-BLAST. ELM server output provides links to the ELM annotation as well as to a number of remote resources. Using the links, researchers can explore the motifs, proteins, complex structures and associated literature to evaluate whether candidate motifs might be worth experimental investigation.

International Supercomputing Conference, Hamburg, Germany 23th June 2009

2009-06-30T21:58:00.000+02:00

The International Supercomputing Conference is the Europe’s premier HPC event. The attendance allows observing trends science and technology of High Performance Computing for whole next year. 2009 edition achieved record numbers of attendees and exhibitors, a level of success even more impressive given the international economic crisis. With its move to Hamburg, ISC’09 reached a significantly higher level of attendance, bringing 1,670 HPC industry leaders. Research labs demonstrated their scientific applications of supercomputing in most recent fields such us GPGPU accelerators, clouds and green computing. Furthermore, this, ISC’09 also welcomed several first-time exhibitors. The exhibition brought countless highlights such as the demo of both the IS5000 40 Gb/s infniband switches and low-latency 10 Gigabit Ethernet. The attendance on ISC’09 allows to anticipate future development of ATLAS system and to present current achievements’ of ToK4nEDA team.

GPGPU Accelerated Sparse Linear Solver for Fast Simulation of On-Chip Coupled Problems

2009-03-29T13:27:00.001+02:00

Continued device scaling into the nanometer region has given rise to new effects that previously had negligible impact but now present greater challenges to designing successful mixed-signal silicon. Design efforts are further exacebated by unprecedented computational resource requirements for accurate design simulation and verification. This paper presents a GPGPU accelerated sparse linear solver for fast simulation of on-chip coupled problems using nVIDIA and ATI GPGPU accelerators on a multi-core computational cluster and evaluate parallelization strategies from a computational perspective.

2nd International Workshop on High Performance Grid Middleware, Bucharest, Romania

2008-11-25T20:34:00.000+01:00

Grid Middleware refers to resource management, execution management, data management, security, monitoring and discovery, accounting, and other functions required by Virtual Organizations to operate effectively a shared services environment. Obtaining high performance Grid Middleware through new, innovative solutions is a challenge of today research, due to the strong requirements imposed by the dynamic behavior of the user and resource communities that compose the Virtual Organizations.
The purpose of the workshop is to provide an open forum for researchers from the Grid middleware community to present, discuss, and exchange research-related ideas, results, and experiences in the area of high performance grid middleware. Establish further subject for cooperation and common project is also at the aim of this workshop.

International Supercomputing Conference, Dresden, Germany

2008-05-25T11:58:00.002+02:00

ISC has evolved into a high-powered international conference and exhibition that gives its attendees a global perspective on the cutting edge of HPC. As always, our conference program tackles hot HPC topics; this year, for example, we will have a panel session on “Green Computing”, a topic that was almost unknown just two years ago. ISC’s focus on future trends and developments can also be seen in this year’s keynote presentation by Prof. Dr. Satoshi Matsuoka of the Tokyo Institute of Technology, Japan, who will discuss “Everybody Supercomputes in the Next Generation Cyber-Science Infrastructure”.
I look forward to seeing you in Dresden.

GOLEM - Grid On computationaL Electro-Magnetics

2008-05-09T12:10:00.001+02:00

The goal of this project is to produce a Beowulf claster of modular computational infrastructute especially designed for Computational Electromagnetics (CEM) . Initially in GOLEM we would like simply a cluster skeleton which could be applied to any preexisting computational code with a minimum effort. Making sure that the code is as portable as possible will hopefully increase the usefulness of the package. Beowulf Cluster widely-used term meaning independent computers combined into a unified system through software and networking based on commodity hardware, on a private system network. One of the main goals of GOLEM project is Design of the advanced PC cluster of Beowulf type and its integration with local and European Grid Network for solving of large system of linear equations by direct (sparse matrices solvers) and iterative methods. The infrastructure will support industry and also other research projects.

The application of graph theory and high performance computing medical diagnostics and nanotechnology

2008-01-22T18:04:00.000+01:00

The commercial application is the integrated system for detection of new regulatory elements located in the non coding genome parts. Until now many human disorders have been found to be connected to some of the noncoding RNA’s. Detection of new noncoding elements and correlation with SNP (Single Nucleotide Polymorphysm) databases may allow help to detect and explain cause of other types of cancer and diseases.
Computational prediction of ncRNAs in genomic sequences would also allow experimental testing of expression levels, functional assay by deletion or mutagenesis, structural analysis and identification of protein or nucleic acid interaction partners.
Another application is so called RNA nanotechnology. It is designing of nanoparticles, which are assembled mainly from ribonucleic acid which possess both the right size and ability to gain entry into cells and halt viral growth or cancer's progress or deliver drugs. Some of those nanoparticles has been successfully tested in mice and lab-grown human cells

Implementation and development of ATLAS Beowulf type cluster network for nano-Electronic Design Automation in ToK4nEDA project

2007-12-19T11:29:00.000+01:00

Beowulf Cluster widely-used term meaning independent computers combined into a unified system through software and networking based on commodity hardware, on a private system network. One of the main goals of ToK4nEDA project is Design of the advanced PC cluster of Beowulf type named ATLAS (Advanced Technology Laboratory Server) and its integration with local and European Grid Network (EUROGRID) for solving of large system of linear equations by direct (sparse matrices solvers) and iterative methods. The infrastructure will support industry and also other research and training projects related to ToK4nEDA such as Chameleon, Artic, Comson and EST.

DATAGENOM 3rd progress meeting - Scotland

2006-10-31T22:12:00.000+01:00

The DATAGENOM project extends from genome analysis, through cloning, expression, enzyme production, screening and protein engineering, to the enzymatic production of chiral biomolecules.

The design of the project takes advantage of broad funnel-approach starting with innovative data-mining and processing of a large number of genes to ensure high flow-through in the process and rational selection of best enzyme candidates. The purpose of this progress meeting of the DATAGENOM project is to report on the progress made for the third period and remaining plans for the final steps and conclusion of the project. Also to define any required assistance between members to complete the work.

Annual SEPSDA Meeting - Beijing, China

2006-10-21T22:03:00.001+02:00

The general objective of the Sino-European Project on SARS Diagnsotics and Antivirals (SEPSDA) is to carry out a complete analysis of the genome and the proteome, including the structural proteome, of the SARS coronavirus and to use the knowledge gained for the rational discovery of antiviral compounds as well as for the development of new, more specific diagnostics.

The meeting was held in Sino-German Center for the Promotion of Science in Beijing and was the important part of the mid-term review of the project.

Analysis tenascin-C for suppression of Human Brain Tumor with Interference RNA

2006-05-28T12:05:00.001+02:00

Glioblastoma multiforme (GBM) accounts for approximately 12-15% of intracranial neoplasms. The GBM remains refractory to therapy because of tumor heterogenity, local invasion, and non-uniform vascular permeability to drugs. Patients with GBM have the median survival of approximately 8-10 months, and for those cases where tumor recurs, the average time of tumor progression after therapy is only eight weeks. A combination of different treatment modes as surgery and chemo- or/and radiotherapy extend survival only for a short time, if any. Recently, tenascin-C (TN-C) as a dominant epitope in glioblastoma has been discovered. Tenascin-C is a multidomain large extracellular matrix glycoprotein composed of six monomers. The size of tenascin-C monomers (180-250kDa) varies as a result of an alternative splicing of the fibronectin repeats at the pre-mRNA level. For the first time we applied bioinformatic and molecular modeling procedures, for detailed analysis of the organization of tenascin-C and we performed bioinformatic analysis of tenascin-C gene. We showed the higher level of tenascin-C in the human tumor tissues: brain, intestine and breast. These results suggested a new role of tenascin-C as the potential tumor marker and drug target.

1st BioScience Partnering Event: Berlin - Brandenburg meets Poznan

2006-03-30T22:48:00.000+02:00

The BioScience Partnering event provided excellent opportunities for researchers and representatives in the area of Life Sciences and Biotechnology from both regions to establish new contacts and joint activities.

The program included presentations of both regions followed by scientific talks about key science activities and important research topics in the Life Sciences. Participants were invited to present a poster at the venue. The initiative BioScience Partnering invited all participants to apply for a traveling grant to bring forward new ideas for bilateral cooperation. Furthermore, the co:bios FOUNDATION offered the possibility for PhD students to participate at a research project in the region Berlin-Brandenburg. The event was jointly organised by the BioScience Partnering initiative of Berlin-Brandenburg together with the Adam Mickiewicz University Poznan (Poland). As an activity in the context of the German-Polish Year the meeting was supported by the Bundesminsterium für Bildung und Forschung (BMBF). For more information please visit our homepage: www.BioScience-Partnering.de

Linki

2005-05-23T02:55:00.000+02:00

Bioinformatics:

An Automated Comparative Protein Modelling Server
NCBI
PubMED
ENTREZ
PSI-BLAST
Protein Data Bank (RCSB)
SCOP
Czasopisma on-line
Institute of Bioorganic Chemistry
Genome News Network
CASP - Submition
T-COFFEE
BioPERL
SWISS MODEL
CMC Modelling Guide
Verify 3D
Enzyme Database - BRENDA
Kyoto Encyclopedia of Genes and Genomes
Dali
Protein Structure Prediction Center
Dunbrack's Culling PDB's
Kinemage Home Page
GlobPlot
Genome Browser
mfold
Biblioteka Wirtualna ICM
PRIDE
TOPS
Primer3

Friends homepages:

Erik Delber
Dylan Chivian
Yuzhen Ye
Lukas the Silvan Archmage
Marcin - Biologia molekularna
Darman - Fizyka
Jachu - Dystanse genetyczne
Scotty - góry i NBA
Lucjan - Genomika
Marcin von Grotthuss - Klastrowanie zwiazków chem.
Wojciech Lasociński
Uciekinierka - strona domowa
Mateusz - fotografia
Ewa Stachowiak
Marcin Feder

Linux:

WLAN
LinuxSky
Samba Domain Control
ASUS A1000
Ruch Na Rzecz Wolnego Oprogramowania
wlan2
wep3
WLAN
LinuxSky
Samba Domain Control
ASUS A1000
Ruch Na Rzecz Wolnego Oprogramowania
wlan2
wep3

Programing:

C++ Manual
Refleksja na temat bezpieczeństwa serwisów internetowych ;)
PHP Manual
PERL Manual
(My)SQL Manual
Fortran 77
Linux C programing
Magic Software