AJAX-based Graphical User Interface for Real-Time PCR Analysis
Introduction
Activities at Swedish Defence Research Agency in Umeå are oriented mainly towards the assessment and evaluation of threats, identification of hazardous substances and verification of their use, and the development of different types of protection. A common tool for robust detection of biological samples is the real-time polymerase chain reaction (PCR), which is used to amplify and quantify specific parts of the DNA contained in the sample. A major advantage of this technique is the sensitivity, but problems with false positive results and inaccurate quantifications are also evident. To mitigate such problems, novel algorithms for analysis real-time PCR data have therefore recently been developed and implemented in the R statistical framework. The lack of a graphical user interface, however, is a major shortcoming that prevents widespread use.
Objective
The objective for this master thesis project is to develop a prototype graphical user interface for semi-automatic analysis of real-time PCR data using AJAX (Asynchronous Javascript And XML) with PHP. This allows use of backend pre-existing implementations of analytical algorithm, safe and simple data storage, and also the possibility of integration into other web-based laboratory information and analysis systems.
Previous knowledge
Previous experience and with Javascript programming is required. A working knowledge of AJAX and R is also an advantage. Most of the work will focus on the development of a graphical user interface. It is important also that you have the ability to work independently.
Contact person:
Pär Larsson
FOI - Swedish Defence Research Agency
CBRN Defence and Security
Cementvägen 20
901 82 Umeå
Telefon: +46-90-106789
Mail:
AJAX-based DNA Assembly Viewer and Editing Tool
Introduction
Activities at the Swedish Defence Research Agency in Umeå are oriented mainly towards the assessment and evaluation of threats, identification of hazardous substances and verification of their use, and the development of different types of protection. Analysis of DNA sequence information for bacterial isolates can reveal past mutation events that can be used to identify and trace and link their origin. Information is usually obtained by assembly of multiple experiments where DNA sequences are aligned. A manual inspection and of the assembly and the underlying data, however, provides increased confidence in the data and manual editing is sometimes also required to correct errors.
There is a need for a simple graphical user interface where scientist can easily view and possibly edit sequence alignments that have been produced on bioinformatics servers.
Objective
The objective for this master thesis project is to implement a prototype AJAX-based graphical user interface to view and edit sequence assemblies. This allows safe and simple data storage, and also the possibility of integration into other web-based laboratory information and analysis systems
Previous knowledge
Previous experience and with Javascript programming is required. A working knowledge of AJAX is also an advantage. Most of the work will focus the development of a graphical user interface. It is important also that you have the ability to work independently.
Contact person:
Pär Larsson
FOI - Swedish Defence Research Agency
CBRN Defence and Security
Cementvägen 20
901 82 Umeå
Telefon: +46-90-106789
Mail: