Wednesday, October 21, 2015

Continous integration with PHP and Jenkins


Continuous integration (CI) is a development practice which allows testing, building and checking the quality of the application in automated way without manual developer intervention. It requires developers to integrate code into a shared repository several times a day or every commit/merge to the given branch of the repository. Each check-in is then verified by an automated build, allowing teams to detect problems early.

While PHP Continuous Integration (PHPCI) does not require the the code compilation as
build” one can understand the set of task like testing and quality checks which are performed in timely manner or when the certain conditions are met.
PHPCI can be performed on Jenkins Server. The detailed description of jenkins server configuration in is presented here. PHPCI requires PHing package which can be provided into application by Composer.

Wednesday, December 11, 2013

Application and implementation of probabilistic profile-profile comparison methods for protein fold recognition

Fold recognition is a method of fold detecting and protein tertiary structure prediction applied for proteins lacking homologues sequences of known fold and structure deposited in the Protein Data Bank. They are based on assumption that there is strictly limited number of different protein folds in nature, mostly as a result of evolution and due to basic physical and chemical constraints of polypeptide chains. Fold recognition methods are useful for protein structure prediction, evolutionary analysis, metabolic pathways and enzymatic efficiency prediction, molecular docking and drug design. Currently there are about 1300 discovered and characterized protein folds in SCOP and CATH databases. Every newly discovered protein sequence has significant chances to be classified into one of those folds. Many different approaches have been proposed for finding the correct fold for a new sequence and it is often useful to include evolutionary information for query as well as for target proteins. One of the methods of including this information is a comparison of a query and target sequences profiles. These fold recognition techniques are called profile-profile methods. Profile-profile alignments can be calculated using a dot-product, a probabilistic model, stochastic or theoretical measures. Here are presented applications and implementations of probabilistic profile-profile comparison methods and advantages of usage of probabilistic scoring function over comparable fold recognition techniques. The purpose of this comparison is to show that probabilistic profile-profile methods may outperform other fold recognition methods in comparison in analysis of distantly related proteins and that they can be applied not only for fold recognition but also for slightly different purposes like gene identification, detection of domain boundaries and modeling of complex proteins.

Thursday, November 10, 2011

GRDB – Gene Relational DataBase

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)
Comprehensive classification of nucleotidyltransferase fold proteins: identification of novel families and their representatives in hum

Monday, October 18, 2010


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.


Friday, January 1, 2010

ELM: the status of the 2010 eukaryotic linear motif resource

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 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.

Tuesday, June 30, 2009

International Supercomputing Conference, Hamburg, Germany 23th June 2009

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.
Jakub Paś
Jakub Paś

Jakub Paś

Jakub Paś
Jakub Paś

Jakub Paś

Sunday, March 29, 2009

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

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.

Tuesday, November 25, 2008

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

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.

Sunday, May 25, 2008

International Supercomputing Conference, Dresden, Germany

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.

Friday, May 9, 2008

GOLEM - Grid On computationaL Electro-Magnetics

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.

Tuesday, January 22, 2008

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

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

Wednesday, December 19, 2007

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

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.
Jakub Paś

Tuesday, October 31, 2006

DATAGENOM 3rd progress meeting - Scotland

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.

Saturday, October 21, 2006

Annual SEPSDA Meeting - Beijing, China

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.

Sunday, May 28, 2006

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

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.