Team:AMU-Poznan/Project
From 2014.igem.org
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expression of cognate mRNAs when expressed in human cells. Mol Cell. 2002 Jun;9(6):1327- | expression of cognate mRNAs when expressed in human cells. Mol Cell. 2002 Jun;9(6):1327- | ||
33</br> | 33</br> | ||
- | <h1>Judging Form</h1> | + | <h1>Judging Form (in <b>bold</b> what we did to achieve gold medal) </h1> |
</br>Bronze. The following 4 goals must be achieved:</br> | </br>Bronze. The following 4 goals must be achieved:</br> | ||
- | Register the team, have a great summer, and have fun attending the Jamboree in Boston.</br> | + | <b>Register the team, have a great summer, and have fun attending the Jamboree in Boston.</br> |
- | Create and share a description of the team's project via the iGEM wiki.</br> | + | Create and share a description of the team's project via the iGEM wiki.</br></b> |
- | Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.</br> | + | Present a Poster and Talk at the Regional Jamboree and World Championship Jamboree.<b> We will on Jamboree :)</br> |
- | Develop and make available, via The iGEM Software Registry, an open source software that supports Synthetic Biology based on Standard Parts.</br></br> | + | Develop and make available, via The iGEM Software Registry, an open source software that supports Synthetic Biology based on Standard Parts.</b></br></br> |
Silver: In addition to the Bronze Medal requirements, the following 4 goals must be achieved:</br> | Silver: In addition to the Bronze Medal requirements, the following 4 goals must be achieved:</br> | ||
- | Demonstrate the relevance of your development for Synthetic Biology based on standard Parts.</br> | + | <b>Demonstrate the relevance of your development for Synthetic Biology based on standard Parts.</br> |
Provide a comprehensive and well-designed User Guide. (Be creative! An instructional video may work as well.)</br> | Provide a comprehensive and well-designed User Guide. (Be creative! An instructional video may work as well.)</br> | ||
Provide detailed API documentation, preferably, automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc).</br> | Provide detailed API documentation, preferably, automatically built from source code documentation (use tools like doxygen, yard, rdoc, naturaldocs, etc).</br> | ||
- | Demonstrate that you followed best practises in software development so that other developers can modify, use and reuse your code. Provide more than one realistic test case. Examples of best practices are automated unit testing and documentation of test coverage , bug tracking facilities, documentation of releases and changes between releases.</br></br> | + | Demonstrate that you followed best practises in software development so that other developers can modify, use and reuse your code. Provide more than one realistic test case. Examples of best practices are automated unit testing and documentation of test coverage , bug tracking facilities, documentation of releases and changes between releases.</br></br></b> |
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> | ||
- | 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>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> |
And the second goal can be any one of the following:</br> | And the second goal can be any one of the following:</br> | ||
Make your software interact / interface with the Registry.</br> | Make your software interact / interface with the Registry.</br> | ||
- | Re-use and further develop previous iGEM software projects (or parts thereof) or use and/or improvement of existing synthetic biology tools or frameworks.</br> | + | <b>Re-use and further develop previous iGEM software projects (or parts thereof) or use and/or improvement of existing synthetic biology tools or frameworks.</br> |
- | Develop a well documented library or API for other developers (rather than “only” a stand-alone app for end users.) | + | Develop a well documented library or API for other developers (rather than “only” a stand-alone app for end users.)</b> |
Support and use the SBOL and / or SBOLv standard.</br> | Support and use the SBOL and / or SBOLv standard.</br> | ||
- | iGEM projects involve important questions beyond the bench, for example relating to (but not limited to) ethics, sustainability, social justice, safety, security, or intellectual property rights. Describe an approach that your team used to address at least one of these questions. Evaluate your approach, including whether it allowed you to answer your question(s), how it influenced the team’s scientific project, and how it might be adapted for others to use (within and beyond iGEM). We encourage thoughtful and creative approaches, and those that draw on past Policy & Practice (formerly Human Practices) activities.</br></br> | + | <b>iGEM projects involve important questions beyond the bench, for example relating to (but not limited to) ethics, sustainability, social justice, safety, security, or intellectual property rights. Describe an approach that your team used to address at least one of these questions. Evaluate your approach, including whether it allowed you to answer your question(s), how it influenced the team’s scientific project, and how it might be adapted for others to use (within and beyond iGEM). We encourage thoughtful and creative approaches, and those that draw on past Policy & Practice (formerly Human Practices) activities.</b></br></br> |
</div> | </div> | ||
Revision as of 16:51, 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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