Team:AMU-Poznan/Project
From 2014.igem.org
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<h1>Releases (re-use of 2013iGEM software)</h1> | <h1>Releases (re-use of 2013iGEM software)</h1> | ||
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- | </br>sh-miR designer v1.0 </br> | + | <h3></br>sh-miR designer v1.0 </br></h3> |
First version of the program presented on iGEM 2013 by our team. The user have to provide siRNA sequence (one or both strands). The miRNA database includes 5 miRNAs. </br> | First version of the program presented on iGEM 2013 by our team. The user have to provide siRNA sequence (one or both strands). The miRNA database includes 5 miRNAs. </br> | ||
- | sh-miR designer v1.1 </br> | + | <h3>sh-miR designer v1.1 </br></h3> |
Strand discrimination functionality was added based on miRbase. </br> | Strand discrimination functionality was added based on miRbase. </br> | ||
extended miRNA database </br> | extended miRNA database </br> | ||
- | sh-miR designer v2.0 </br> | + | <h3>sh-miR designer v2.0 </br></h3> |
siRNA prediction algorithm was added to functionality (the input is NCBI transcript number) </br> | siRNA prediction algorithm was added to functionality (the input is NCBI transcript number) </br> | ||
user can choose GC content of siRNA molecule, maximal off-target, if he/she wants immunostimulatory sequences inside the molecule and to choose if he/she wants to include all or chosen scaffold </br> | user can choose GC content of siRNA molecule, maximal off-target, if he/she wants immunostimulatory sequences inside the molecule and to choose if he/she wants to include all or chosen scaffold </br> | ||
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</br> | </br> | ||
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+ | <pre> | ||
In our application we are using unit tests to test alghoritms, functions and database.</br> | In our application we are using unit tests to test alghoritms, functions and database.</br> | ||
We are testing inputs and outputs:</br> | We are testing inputs and outputs:</br> | ||
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)</br> | )</br> | ||
</br> | </br> | ||
+ | </pre> | ||
</div> | </div> | ||
<h1>Validation</h1> | <h1>Validation</h1> | ||
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</ul> | </ul> | ||
Gold: In addition to the Bronze and Silver Medal requirements, two additional goals must be achieved: </br> | Gold: In addition to the Bronze and Silver Medal requirements, two additional goals must be achieved: </br> | ||
- | <b>Provide a convincing validation, testing the performance of the development -- experimentally (can be outsourced) or by other teams and users. Note, even if the algorithm or tool turns out not to work that well, the Gold requirement is fulfilled if the test is good and the analysis convincing. Validation may include: preferably experiments, informatics analysis (complexity, run time) of an algorithm, or user studies.</br></b> | + | <b><ul><li>Provide a convincing validation, testing the performance of the development -- experimentally (can be outsourced) or by other teams and users. Note, even if the algorithm or tool turns out not to work that well, the Gold requirement is fulfilled if the test is good and the analysis convincing. Validation may include: preferably experiments, informatics analysis (complexity, run time) of an algorithm, or user studies.</li></ul></br></b> |
And the second goal can be any one of the following:</br> | And the second goal can be any one of the following:</br> | ||
<ul> | <ul> |
Revision as of 17:48, 15 October 2014
sh-miR Designer v2.0Sh-miR designer is a project we started during iGEM 2013. This year we would like to continue and expand functionality of the software. sh-miR designer v1.0 (link) is aimed to create sh-miR molecules based on siRNAs provided by the user. In sh-miR designer v2.0 only the mRNA number (from NCBI database), which expression should be decreased can be provided. Moreover, we expanded functionality of the software with off-target validation and check of immune motifs and also extended miRNA-shuttles database. sh-miR Designer is a software aimed for fast and efficient design of effective RNA interference (RNAi) reagents - sh-miRs, also known as artificial miRNAs. sh-miRs are RNA particles whose structure is based on miRNA precursor pri-miRNA, but sequence interacting with transcript is changed depending on research purpose. Maintenance of structure of pri-miRNA is very important to enable cellular processing and therefore ensure functionality of artificial particles. sh-miRs delivered to cells on genetic vectors - plasmids or viral vectors - enter natural RNAi pathway and silence target mRNA. They can be used in genetic therapies and basic biomedical research. We will provide two applications to access the software, one which require siRNA sequences and the second which require transcript accession number from NCBI database. Each user will receive an account with login (e-mail) and password where he/she would be able to check history of software usage.input form: users' history: Standard PartsWe are creating a particle which can be inserted into plasmid built by Standard parts from Registry of Standard Biological Parts.User GuideUsage via Web server
go to our website shmir.wmi.amu.edu.pl
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