Marcelina Borcz

Heteroplasmic substitutions in the entire mitochondrial genomes of human colon cells detected by ultra-deep 454 sequencing

Mitochondrial DNA (mtDNA) heteroplasmy has been widely described from clinical, evolutionary and analytical points of view. Historically, the majority of studies have been based on Sanger sequencing. However, next-generation sequencing technologies are now being used for heteroplasmy analysis. Ultra-deep sequencing approaches provide increased sensitivity for detecting minority variants. However, a phylogenetic a posteriori analysis revealed that most of the next-generation sequencing data published to date suffers from shortcomings. Because implementation of new technologies in clinical, population, or forensic studies requires proper verification, in this paper we present a direct comparison of ultra-deep 454 and Sanger sequencing for the detection of heteroplasmy in complete mitochondrial genomes of normal colon cells. The spectrum of heteroplasmic mutations is discussed against the background of mitochondrial DNA variability in human populations.

Seamless access to the PL-Grid e-infrastructure using UNICORE middleware

This chapter provides a brief overview of the UNICORE grid middleware and its utilization in the large Distributed Computing Infrastructure. UNICORE framework, in its recent version implements key grid standards and specifications. The system architecture and capabilities, such as security, workflow and data management are described. The installation of the UNICORE environment in the PL-Grid is presented. Special attention is given to the integration of the UNICORE middleware with the PL-Grid authentication and authorization framework which allows for uniform infrastructure and user management across different middlewares. The solutions for monitoring and accounting of the UNICORE infrastructure is presented.

Development of Domain-Specific Solutions Within the Polish Infrastructure for Advanced Scientific Research

The Polish Grid computing infrastructure was established during the PL-Grid project (2009–2012). The main purpose of this Project was to provide the Polish scientists with an IT basic platform, allowing them to conduct interdisciplinary research on a national scale, and giving them transparent access to international grid resources via international grid infrastructures. Currently, the infrastructure is maintained and extended within a follow-up PLGrid Plus project (2011–2014). Its main objective is to increase the potential of the Polish Science by providing necessary IT services for research teams in Poland, in line with European solutions. The paper presents several examples of the domain-specific computational environments, developed within the Project. For particular environments, specialized IT solutions are prepared, i.e. dedicated software implementation and infrastructure adaptation, suited for particular researchers groups’ demands.

Grid services for genomic research. Polish national grid perspective

In this paper we present grid services for the biomolecular community offered by the Polish National Grid (Polish NGI). This work is motivated by the fact that in many application areas including life sciences there is increasing demand for disk space and computer power to store and process data. Emerging technologies such as Next Generation Sequencing (NGS) put additional stress on this demand. The amount of data which biologists have to handle is usually too big to be stored and processed in the laboratory using desktop or even more powerful single computers. The ultimate solution is grid technology offering seamless access to the distributed storage and computational resources. There has been number of different grid infrastructures used. The solution built using UNICORE middleware is example of the most successful one. In this paper we present the UNICORE installation in the Polish NGI. We provide details of the middleware deployment on the PL-Grid infrastructure. Overview of the bioinformatics related services is extended by the details of the grid deployment of the widely used bioinformatic applications such as BLAST. We also provide description of the grid infrastructure and services developed to support gene sequencing and its use in the diagnostics process. The storage and computational grid services are fully integrated with the sequencing equipment to make whole process seamless and easy to use. The described solution allowed to simplify analysis of sequencing results and make them available in the short time feasible for medical diagnosis.

Training in the PL-Grid as key component to attract users to grid e-infrastructures

This chapter provides an overview of the training facilities in the PL-Grid project. It is well known that procedures necessary to obtain certificates and then install software or get access to the User Interfaces are complicated and due to security reasons cannot be simplified. For these purposes we have crated extended training facilities which allow to get easy access to the Grid. We have installed dedicated infrastructure including the computational resources, certificate authority, user portal and an on-line training system. The efficiency of the training infrastructure, materials and procedures has been proved in the numerous training sessions.