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ViFrame

 

ViFrame

Type: 
Bioinformatics & Cheminformatics
One line description: 
Chemical space visualization framework
Annotation: 

 

ViFrame is a modular framework targeted at chemical space visualization task. It offers a simple implementation of every single part of the visualization pipeline consisting of steps such as reading and merging molecules from multiple data sources, applying transformations and finally visualization of the data set in 2D space. The framework also incorporates an application that provides the user with graphical
interface for modules manipulation and presentation of the visualization results. For simple utilization of the application without the necessity of implementation of one’s own module, several visualization methods are implemented and delivered with the project.
Developers: 
david.hoksza
petr.skoda

Security seminar AFCEA on topic BIG data, Police Academy of the Czech Republic, Prague, 2012

Date: 
27.11.2012

RNDr. Jakub Lokoč Ph.D. has presented an invited talk about similarity search problems in huge multimedia collections at the security seminar BIG DATA, organized by the Police Academy of the Czech Republic in Prague, 27.11.2012. More information about the seminar available here (CZ) - stránkách akce.

Jeden den s informatikou 2012 (in czech)

Date: 
19.09.2012

Přednášky:

  • David Hoksza: Bioinformatika a cheminformatika na MFF

PGRTree homepage

Introduction

In commercial database platforms, the standard search over multiple attributes is provided by B+-tree (or it’s variants) with compound keys. On the other hand, such systems provide also multidimensional indexing, however, just for spatial purposes (such as GIS or CAD applications) and use special data types and querying syntax. Our solution allows to apply R-tree index (hence multi-dimensional indexing structure) in the same way as B+-tree with compound keys is applied. The solution is delivered as a plugin for PostgreSQL database.

PGRTree

Type: 
General indexing
One line description: 
Plugin for Indexing Multidimensional Data in PostgreSQL Using R-tree
Annotation: 

In commercial database platforms, the standard search over multiple attributes is provided by B+-tree (or it’s variants) with compound keys. On the other hand, such systems provide also multidimensional indexing, however, just for spatial purposes (such as GIS or CAD applications) and use special data types and querying syntax. Our solution allows to apply R-tree index (hence multi-dimensional indexing structure) in the same way as B+-tree with compound keys is applied. The solution is delivered as a plugin for PostgreSQL database.

Developers: 
david.hoksza

Molpher

Type: 
Bioinformatics & Cheminformatics
One line description: 
Software tool for exploration of the chemical space
Annotation: 

Molpher aims to be a scalable and interactive software tool to aid exploration of chemical space, the vast universe containing all possible compounds. Many areas of chemical biology, such as drug discovery, rely heavily on chemical libraries offering compounds usable in the industrial processes. Given a set of molecules with desired characteristics, Molpher explores their common neighbourhood based on structural similarity, as it represents promising part of the chemical space to find new additions into those libraries. In order to decrease the chance of missing interesting parts of the space, Molpher offers the human researcher to observe and interactively alter the exploration process. Generated subspace is expected to be further tested for synthesizability and biological activity by other software tools.

Among main features, Molpher offers optimized parallel exploration algorithm, compound logging, dimension-reduced visualization of chemical space and interactive widget-based GUI. Codebase is extensible in terms of additional morphing operators, chemical fingerprints, similarity measures and visualization strategies to allow further experiments.

Developers: 
david.hoksza
petr.skoda

Teaching VSFS

Teaching UK

Ročníkové, diplomové a bakalářské práce

Zájemci o BP/DP/SW projekt jsou vítaní, vhodné téma vybráno po ústní konzultaci. Obecně se jedná o témata řešící problematiku podobnostního vyhledávání, multimediální explorace, indexování, atd.

Radoslav Krivák

Name: 
Radoslav
Surname: 
Krivák
Homepage: 
http://siret.ms.mff.cuni.cz/members/krivak/
Research interests: 
  • structural bioinformatics
  • artifical intelligence
  • evolutionary algorithms
  • machine learning
Type of member: 
Student
State: 
Active
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