Self-driven web technologist and cross-platform solutions enthusiast with strong analytic mind. Interest in pattern recognition and integration between web platforms and databases. PhD and Engineering degrees in fields of chemistry / bioinformatics with a strong publication record in peer-reviewed journals. Java, Python & PHP programmer. Keen on rock music and rock climbing
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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.
Overview 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.
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
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 Ja