CS / EN
Probes & Drugs
The Probes & Drugs portal (P&D) is a hub for the integration of high-quality bioactive compound sets enabling their analysis and comparison. Its main focus is on chemical probes and drugs but it also includes additional relevant sets from specialist databases/scientific publications, and vendor sets. Upon these, established bioactive chemistry sources (such as ChEMBL, BindingDB, Guide To Pharmacology, DrugCentral or DrugBank) are utilized for compounds' biological annotation. As of ver. 04.2021, the P&D compound database is composed of 76 sources including 14 probe-related, 8 drug compilations, 37 academic/non-commercial sets and 15 precompiled sets from bioactive compound vendors.
Released
2017
URL
probes-drugs.org
Twitter
@probesanddrugs
Data license
CC BY-SA 4.0
HOW TO CITE
Skuta C, Popr M, Muller T, Jindrich J, Kahle M, Sedlak D, Svozil D, Bartunek P. (2017) Probes & Drugs Portal: an interactive, open data resource for chemical biology. Nature Methods 14(8), pp.759-760. http://dx.doi.org/10.1038/nmeth.4365
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European Chemical Biology Database
The European Chemical Biology Database (ECBD) is the central data hub for data generated within the EU-OPENSCREEN network developed by CZ-OPENSCREEN. It is a web portal with powerful search and analysis capabilities containing validated output from screening centres in a public as well as pre-release environment.The ECBD is developed in line with the FAIR principles ensuring Findability, Accessibility, Interoperability, and Reusability of the data.
The ECBD supports curation, annotation and organization of data and metadata. The data is deposited with a flexible privacy model for rapid and safe dissemination and exploitation. Users stay owner of their data. The optional hold period is 36 months for data publication. There are high standards of security and traceability of IP (citable indexing of data points (EUOS, DOI or URL) and links to originator labs for primary raw unprocessed data.
Released
2021
URL
ecbd.eu
Data license
CC BY-SA 4.0
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Zebrabase
Zebrabase is a scalable, cross-platform fish tracking database developed especially for research fish facilities. It is built on three main cornerstones - comprehensive animal tracking, interactive breeding history and advanced management features.
Our aim is to provide a robust tracking solution for various research infrastructures.Zebrabase is suitable both for small, budget-conscious facilities as well as for large facilities looking to improve workflow management and reporting. Zebrabase supports both desktop and mobile use on various platforms.
Zebrabase has been developed at the Institute of Molecular Genetics in Prague (Czech Republic) by an interdisciplinary team of zebrafish researchers, programmers and web designers. Initially designed as a solution for our own zebrafish facility, we now aim to provide this tracking system to fish facilities worldwide.
Released
2016
URL
zebrabase.org
Data license
CC BY-SA 4.0
HOW TO CITE
Oltova J, Jindrich J, Skuta C, Svoboda O, Machonova O, Bartunek P. Zebrabase: An Intuitive Tracking Solution for Aquatic Model Organisms. Zebrafish. 2018 Sep 20. PubMed, DOI
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CORONAbase
CORONAbase is a comprehensive, cross-platform database for PCR diagnostics, which has been developed and employed at the Institute of Molecular Genetics, Prague, during the COVID-19 pandemic to keep the testing records organized.
It allows to efficiently track patient samples throughout the whole testing process: from sample registration through RNA isolation and qPCR detection, to the final quality control and data reporting. Individual samples are labelled with barcodes that serve as unique identifiers and the application can be adjusted to different workflows based on individual test tubes or multiwell plates. Finally, the interactive plate view gives a visual overview of the occupancy and consistently color coded sample priorities.
CORONAbase provides cross-platform access via webbrowser, as well as full touch support for mobile devices, which makes it easy to quickly navigate through the application from a wide range of devices. The process of sample registration has been optimized for tablets as a practical alternative for entering data in biosafety areas.
Released
2020
URL
coronabase.org
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ScreenX
ScreenX is a LIMS (Laboratory Information Management System) used for the management of chemical-biological data. It is capable of storing information about chemical samples, their properties and structures, substructure and similarity searching, organizing samples into chemical plates, handling of 1D and 2D barcodes for samples and plates, plate reformat (clone, serial dilution, Z-reformat), creating assay plates and arranging them into biological experiments, automatic import of result data to experiments, experiment visualisation and analysis (dose-response curves computation, fragment analysis, cluster analysis, etc.).
Released
-
URL
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Other
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InCHlib
InCHlib (Interactive Cluster Heatmap library) is an open source interactive Javascript library which provides an easy way to display and analyze hierarchically clustered data and cluster heatmaps. It implements a raster-based HTML5 canvas visualization using the open source Javascript framework KonvaJS. InCHlib is multiplatform and works in all major internet browsers (Internet Explorer, Mozilla Firefox, Google Chrome, Safari, Opera). Its speed is determined by the client’s hardware and internet browser. For smoothest user experience, we recommend Google Chrome.
Released
2014
URL
openscreen.cz/software/inchlib
License
The MIT License
HOW TO CITE
Škuta, C.; Bartůněk, P.; Svozil, D. InCHlib – interactive cluster heatmap for web applications. Journal of Cheminformatics 2014, 6 (44), DOI: 10.1186/s13321-014-0044-4.
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ChemSpace
ChemSpace is an open source interactive Javascript library which provides an easy way to display and analyze 2D chemical space within a web page. It implements a raster-based HTML5 canvas visualization using the open source Javascript framework KonvaJS. ChemSpace is multiplatform and works in all major internet browsers (Edge, Mozilla Firefox, Google Chrome, Safari, Opera). Its speed is determined by a client’s hardware and internet browser. For the smoothest experience, we recommend to use Google Chrome.
Released
2016
URL
openscreen.cz/software/chemspace
License
The MIT License
3
RackScanner
RackScanner can read images from configurable directory or directly operate a scanner. RackScanner first localizes the wells of the rack by pattern matching and recognizes the type of the rack. It then determines which wells are empty and which contain barcoded tubes. Attempts to locate and digitize barcodes are then made by three different algorithms using the excellent and fast opencv library. Decoding is done by libdmtx library which also serves as fallback in case that previous attempts to locate the code fail. You can download RackScanner at GitHub.
Released
2017
URL
github.com/michalkahle/RackScanner
License
The MIT License