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Our students' Bachelor and Diploma Thesis

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Electronic publications are gradually replacing the classical paper ones. Unfortunately, at this moment there are many different reading devices with different requirements. Therefore, there is a strong requirement for a single format usable at many devices and ePub format could fulfill this task. This work deals with the ePub specifications and their use for creation of an electronic publication. This way it is possible to investigate advantages and disadvantages of this format and its use in current reading devices (e.g. FBReader). The final result of this work is an electronic publication defining more important properties of ePUB format presented both as printed and electronic book.

There is a rapidly growing number of web documents today and we have a need to organize and be able to process this data. The current web is very limited in this regard. The aim of the Semantic Web is address the issue and provide machine readable information. The cooperation between humans and computers will be improved and automatic processing of data will be simplified with help of this information. The aim of this work is to carry out a thorough research of more widely used formats for creating the Semantic Web with an emphasis on the use of XML technologies. These technologies are then applied to specific examples.

Expansion of OPIUM program for computing of association constants of synthesized compounds. We got a user-friendlier text interface – XML template, where we can fill the needed data in words. Then we transform the XML template by the XSL template and we modified the output file in some text editor a little and then we are petting the input file for OPIUM program.

This thesis is concerned with the creation of software background that is suitable for cheminformatics in terms of testing and teaching. Theories of user accessability and ergonomics are also addressed as well as concrete procedures used for the imple- mentation of such designs. Copyright laws and lincenses protecting individual software products were taken into account together with their e ect on the whole distribution, which had major in uence on choices concerning software addition. The original design was to create a virtual machine and distribute the whole system as a virtual disc image. A python script capable of searching, brie y describing and installing included software has been created and designed to be controlled by user text input. All install les are stored locally in order to allow full oine usage, functionality and the option to rollback to last working version, but the script does also cooperate with package managers and tries to nd and install a newer version from online repo- sitories, if possible. Failing that, the script installs desired software from local sources. Records concerning available software and its description, search keywords and install methods are stored in a XML le. This approach has, however, proven to cause problems during testing on di erent machines. Installed VirtualBox in nonstandard con guration was needed for its functi- oning, and even then the necessary procedures to import system snapshots were not trivial. All those additional complications go against the primary purpose of this thesis: improving accessability. The form of linux LiveDVD distribution has proven to be a suitable alternative, mostly for its much lower software requirements and wider possi- bilities of usage. The result of this thesis is a freely distributable linux LiveDVD containing basic cheminformatic tools and libraries. It is usable for testing, teaching and cheminforma- tic work as well as general, personal use, because the base systems capacity is fully preserved.

This bachelor thesis aims to provide an overview of chemical visualization software with an emphasis on support for stereoscopic output and on the basis of this review select applications that will be suitable for use in a computer lab A30 equipped with a 3D projector. In the practical part of the work is a concept of integration of three-dimensional content into a presentation. It is designed to give the user an option which applications should be used and to allow use of remote presenter to control whole process of presenting 3D content.

The aim of the work is to develop the web application for inorganic crystal structures vizualization. The system will be capable of displaying crystals of inorganic compounds with various crystal symmetry. Crystal structures will either be obtained from the appropriate crystallographic database or the user will be able to vizualize its own structures stored in cif and other data formats. The positions of symmetry equivalent atoms will have to be calculated for proper vizualization. The application will be implemented using the Django web framework and the Javascript library JQuery. The vizualization will be realized by the JMol Java applet.

The main goal of this work was to develop a new chemical XML (Extensible Markup Language) format based on the analysis of current alternatives. I created necessary software tools for performing the detailed analysis of chosen XML formats. This allowed me to identify concepts and prepare interactive references for analysed XML formats. Than I used obtained concepts to design the new XML format for recording the structure and properties of chemical molecules. Compared to current alternatives it provides easy to learn extensible functionality and strict automatized validation to minimize possible mistakes in chemical data.

The aim of this study is to compare in silico methods for the prediction of toxicological properties of chemical substances as an alternative to experimental studies on living organisms. These methods are examined in terms of their use for the purposes of REACH and CLP legislation. European Commission regulations REACH and CLP impose obligations on producers and importers to register and notify chemical substances and mixtures marketed in the European Union. An essential part of the registration is to evaluate the toxicological properties of the substances and mixtures. Testing toxicity on living organisms is considered as the least ethical possibility that is to be avoided and replaced by alternative in silico methods where reliable toxicity predictions can be made. This work focuses on (Q)SAR and read-across methods and demonstrates their usability, strengths and limitations by classification of 37 chemical substances. Research of methods for prediction of toxicity of chemical substances has been greatly encouraged by the REACH and CLP coming to force and are these methods are considered crucial to successful fulfillment of the obligations arising from REACH and CLP, since the in vivo experimental testing of all substances marketed in the European Union is unethical, time consuming and expensive.

Polythematic structured subject heading system (PSH) is czech-english controlled vocabulary managed at the National technical library (NTL). PSH is primarily intended as a tool for manual indexing of documents at NTL and other memory institurions. Its current version (PSH 3.0) contains over 13 800 subject headings divided into 44 categories which cover the main aspects of human knowledge. The aim of this work is the automation and standardization of its content update and management including development of software tools. Integration of PSH to other projects is also investigated.

Title Author Supervisor Type Year
Structural properties of the protein-DNA interface

Sedlák Filip Svozil Daniel bachelor thesis 2009/2010
Datatype library for validation of chemical informatics data

Voršilák Milan Jirát Jiří bachelor thesis 2009/2010
Graphical representation of macromolecular organic substances

Filip Martin Jirát Jiří bachelor thesis 2009/2010
Publishers of scientific journals

Pohunková Petra Nič Miloslav bachelor thesis 2009/2010
Citation analysis of the fourth assessment report of IPCC

Hrotková Radka Nič Miloslav diploma thesis 2009/2010
Software system for identification of names of organic compounds in scientific articles

Glemba Josef Svozil Daniel diploma thesis 2009/2010
Electronic support of the education at the ICT

Znamenáček Jiří Svozil Daniel diploma thesis 2009/2010
Review of ePub format (electronic books)

Maršíková Lucie Nič Miloslav bachelor thesis 2010/2011
Semantic Web technologies

Motejlková Anna Nič Miloslav bachelor thesis 2010/2011
Software for computation of association constants

Kalčicová Andrea Nič Miloslav bachelor thesis 2010/2011
Portable computer environment for processing of chemical data

Čmelo Ivan Jirát Jiří bachelor thesis 2010/2011
Use of 3D visualization software for teaching at ICT Prague

Skalický Jaroslav Jirát Jiří bachelor thesis 2010/2011
Web application for vizualization of crystal structures of inorganic compounds

Müller Tomáš Svozil Daniel diploma thesis 2010/2011
Development of a chemical format for markup of chemical data

Mokrý Jan Nič Miloslav diploma thesis 2010/2011
Predicting Skin Irritation / Corrosion - a Comparison of in silico Methods for Implementing REACH and CLP Legislation

Novotný Tomáš Svozil Daniel diploma thesis 2010/2011
Implementation of Polythematic Structured Subject Heading System in National Technical Library

Škuta Ctibor Nič Miloslav diploma thesis 2010/2011

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