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| <p>In order to stimulate one's inspiration in synbio work design, we tried the following explorations: The tree of words, and network analysis.</p> | | <p>In order to stimulate one's inspiration in synbio work design, we tried the following explorations: The tree of words, and network analysis.</p> |
| <p><b>The tree of words:</b> When you first enter the search engine of S-Din, you could search any word you like, or try selecting a word to explore more! When clicking, You will see the subordinated words. After few repeats, you will finally get the projects that you want. This function is designed to help specify your need, and help you understand your idea better.</p> | | <p><b>The tree of words:</b> When you first enter the search engine of S-Din, you could search any word you like, or try selecting a word to explore more! When clicking, You will see the subordinated words. After few repeats, you will finally get the projects that you want. This function is designed to help specify your need, and help you understand your idea better.</p> |
− | <img src="https://static.igem.org/mediawiki/2017/4/45/T--SYSU-Software--hp_keyword-hierarchy.png" alt="" class="middle centered black-shadowed"> | + | <img src="https://static.igem.org/mediawiki/2017/1/15/T--SYSU-Software--project-keywords.jpg" alt="" class="middle centered black-shadowed"> |
| <p class="fig-ep center">Figure 11: The tree of words.</p> | | <p class="fig-ep center">Figure 11: The tree of words.</p> |
| <p><b>Network analysis: </b>This function is designed to help you find out potential relationships between two parts, projects or keywords. Sometimes the recommendation may be hard to understand, but perhaps it would open a new direction and lots of inspiration for you.</p> | | <p><b>Network analysis: </b>This function is designed to help you find out potential relationships between two parts, projects or keywords. Sometimes the recommendation may be hard to understand, but perhaps it would open a new direction and lots of inspiration for you.</p> |
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| <section class="plain" id="integrated-human-practice"> | | <section class="plain" id="integrated-human-practice"> |
| <h2>Integrated Human Practice</h2> | | <h2>Integrated Human Practice</h2> |
− | <p>S-Din is a product born for solving synthetic biological problems and serving the biologists and ordinary people who are interested in synthetic biology. In our "Integrated Human Practices" page, we'll show essential human practices work we have done around S-Din, including user needs analysis, function improvement for user feedback, product assessment and public promotion.</p> | + | <p>S-Din is a product born for solving synthetic biological problems and serving the biologists and ordinary people who are interested in synthetic biology. In our "Integrated Human Practices" page, we'll show essential human practices work we have done around S-Din, including user needs analysis, function improvement for user feedback, product assessment, and public promotion.</p> |
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| <h3>User needs analysis</h3> | | <h3>User needs analysis</h3> |
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| <h4 id="nju-practice">Study the needs of other iGEM teams & ordinary bio-lovers</h4> | | <h4 id="nju-practice">Study the needs of other iGEM teams & ordinary bio-lovers</h4> |
| <div class="paragraph"> | | <div class="paragraph"> |
− | <p>In the discussion with SYSU-CHINA iGEM team and SCAU-China iGEM team, we reached agreement that fragmented data makes it time-consuming and laborious to collect and reuse data. (<a href="https://2017.igem.org/wiki/index.php?title=Team:SYSU-Software/HP/Silver">Silver page</a>)</p> | + | <p>In the discussion with SYSU-CHINA iGEM team and SCAU-China iGEM team, we reached an agreement that fragmented data makes it time-consuming and laborious to collect and reuse data. (<a href="https://2017.igem.org/wiki/index.php?title=Team:SYSU-Software/HP/Silver">Silver page</a>)</p> |
| <p>Nowadays data or information online is abundant but scattered. Many people spend much time on integrating them by themselves. instead of spending more time on their ideas for their core work. </p> | | <p>Nowadays data or information online is abundant but scattered. Many people spend much time on integrating them by themselves. instead of spending more time on their ideas for their core work. </p> |
| <img class="ui image middle centered" src="https://static.igem.org/mediawiki/2017/5/5a/T--SYSU-Software--hp_fig12.png"> | | <img class="ui image middle centered" src="https://static.igem.org/mediawiki/2017/5/5a/T--SYSU-Software--hp_fig12.png"> |
| <p class="fig-ep center">Figure 13: How a man may assign his time in a project when getting integrated data by himself</p> | | <p class="fig-ep center">Figure 13: How a man may assign his time in a project when getting integrated data by himself</p> |
− | <p>In fact, this trouble is possible to be solved ---- by a dedicated software. If we could establish an integrated database, consisting of unified standard of data composition and data format, we should find out the relationships among the data more easily. Besides, a data format standard makes it more convenient and engineering to store, reuse and combine the data. And engineering work is what computers are good at. </p> | + | <p>In fact, this trouble is possible to be solved ---- by a dedicated software. If we could establish an integrated database, consisting of a unified standard of data composition and data format, we should find out the relationships among the data more easily. Besides, a data format standard makes it more convenient and engineering to store, reuse and combine the data. And engineering work is what computers are good at. </p> |
− | <p>So our team desired to change the work flow into the figure below: </p> | + | <p>So our team desired to change the workflow into the figure below: </p> |
| <img class="ui image middle centered" src="https://static.igem.org/mediawiki/2017/1/17/T--SYSU-Software--hp_fig13.png"> | | <img class="ui image middle centered" src="https://static.igem.org/mediawiki/2017/1/17/T--SYSU-Software--hp_fig13.png"> |
| <p class="fig-ep center">Figure 14: How a man may assign his time in a project when getting integrated data with a dedicated software.</p> | | <p class="fig-ep center">Figure 14: How a man may assign his time in a project when getting integrated data with a dedicated software.</p> |
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| <p>At the same time, we chatted with some students who are interested in biology work. They told us: </p> | | <p>At the same time, we chatted with some students who are interested in biology work. They told us: </p> |
| <p class="quote">"We'll like the software if it shows details of each bio-project, in a way easy to understand."</p> | | <p class="quote">"We'll like the software if it shows details of each bio-project, in a way easy to understand."</p> |
− | <p class="quote">"It would be better if the software can provide basic analysis of the work."</p> | + | <p class="quote">"It would be better if the software can provide a basic analysis of the work."</p> |
| <p class="quote">"Could you develop a software which can recommend interesting projects of my own?"</p> | | <p class="quote">"Could you develop a software which can recommend interesting projects of my own?"</p> |
| <p class="quote">...</p> | | <p class="quote">...</p> |
− | <p>We found that the needs above are the most popular. To achieve these goals, an enough huge and integrated database is critical. Of course, mathematical algorithms should be equipped in our software. </p> | + | <p>We found that the needs above are the most popular. To achieve these goals, an enough huge and integrated database is critical. Of course, mathematical algorithms should be equipped with our software. </p> |
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| <h4>Studying the needs of biology labs</h4> | | <h4>Studying the needs of biology labs</h4> |
| <p>During the summer, we visited several biology laboratories of Sun Yat-sen University. Researchers warmly greeted us. Thanks to Prof. Lu Yongjun's help, we finished our interlab task and wet-lab validation in his laboratory. Meanwhile, we chatted with the researchers and conducted a small survey of their project idea. </p> | | <p>During the summer, we visited several biology laboratories of Sun Yat-sen University. Researchers warmly greeted us. Thanks to Prof. Lu Yongjun's help, we finished our interlab task and wet-lab validation in his laboratory. Meanwhile, we chatted with the researchers and conducted a small survey of their project idea. </p> |
| <p>By talking with researchers working in the lab, we were surprised that lack of ideas is one of the common problems when they work on a synthetic biology project. </p> | | <p>By talking with researchers working in the lab, we were surprised that lack of ideas is one of the common problems when they work on a synthetic biology project. </p> |
− | <p><span class="quote">“A good beginning is half done. That is to say, a good idea of genetic circuit design is half done of the whole project.”</span> A researcher named Dong told us. </p> | + | <p><span class="quote">“A good beginning is half done. That is to say, a good idea of a genetic circuit design is half done of the whole project.”</span> A researcher named Dong told us. </p> |
| <p>Since ideas are so significant to a project, where do researchers' ideas usually come from? We did a small survey of researchers in several labs. </p> | | <p>Since ideas are so significant to a project, where do researchers' ideas usually come from? We did a small survey of researchers in several labs. </p> |
| <img class="ui image middle centered" src="https://static.igem.org/mediawiki/2017/c/c6/T--SYSU-Software--hp_idea-source.png" alt="not provide"> | | <img class="ui image middle centered" src="https://static.igem.org/mediawiki/2017/c/c6/T--SYSU-Software--hp_idea-source.png" alt="not provide"> |
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| <p>From the figures above, we learned that the majority of researchers’ idea source is professional research articles and journals ---- <span class="bold">they work before, but a novel idea may arouse from them if the researcher reuses their essence and aims to an accessible direction.</span> However, each paper usually describes its design in the author’s own style and standard, which is usually hard to understand and absorb its design ideas for one’s own creative work. </p> | | <p>From the figures above, we learned that the majority of researchers’ idea source is professional research articles and journals ---- <span class="bold">they work before, but a novel idea may arouse from them if the researcher reuses their essence and aims to an accessible direction.</span> However, each paper usually describes its design in the author’s own style and standard, which is usually hard to understand and absorb its design ideas for one’s own creative work. </p> |
| <p><span class="quote">“We all hope to stand on shoulders of the giant, but it's hard at this stage to combine or transfer the senior's ideas in order to form my own ideas.”</span> Researcher Dong said. </p> | | <p><span class="quote">“We all hope to stand on shoulders of the giant, but it's hard at this stage to combine or transfer the senior's ideas in order to form my own ideas.”</span> Researcher Dong said. </p> |
− | <p>How to trigger one's inspiration? What if our software could help people with inspiration? This "Inspiration" inspires all of us. However, it is a challenge for us, because “inspiration” is such an abstract concept, and is hard to measure and specify. But hope is still alive: several related previous work may create a new idea. To find out related projects and to guide users to a clearer direction, are what we consider to achieve in our software. </p> | + | <p>How to trigger one's inspiration? What if our software could help people with inspiration? This "Inspiration" inspires all of us. However, it is a challenge for us, because “inspiration” is such an abstract concept, and is hard to measure and specify. But hope is still alive: several related previous works may create a new idea. To find out related projects and to guide users to a clearer direction, are what we consider to achieve in our software. </p> |
| <p>Thanks to the inspiration flashed across our mind, we decided to create an onomatopoeia "S-Din" as the name of our project and software, as it sounds like turning on a bulb. </p> | | <p>Thanks to the inspiration flashed across our mind, we decided to create an onomatopoeia "S-Din" as the name of our project and software, as it sounds like turning on a bulb. </p> |
| </div> | | </div> |
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| <h4>Integrated database</h4> | | <h4>Integrated database</h4> |
| <div class="paragraph"> | | <div class="paragraph"> |
− | <p>In S-Din's database, we standardize a new data format for different types of data: parts, projects, key words and papers. Based on this format, our database is integrated into a unity, and accessible to set up interaction network and analysis. The S-Din search engine and S-Din Design are both working under this standard.</p> | + | <p>In S-Din's database, we standardize a new data format for different types of data: parts, projects, keywords and papers. Based on this format, our database is integrated into a unity, and accessible to set up interaction network and analysis. The S-Din search engine and S-Din Design are both working under this standard.</p> |
| </div> | | </div> |
| <h4>Keyword Tree & Network Analysis</h4> | | <h4>Keyword Tree & Network Analysis</h4> |
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| <p>In order to stimulate one's inspiration in synbio work design, we tried the following explorations: The tree of words, and network analysis.</p> | | <p>In order to stimulate one's inspiration in synbio work design, we tried the following explorations: The tree of words, and network analysis.</p> |
| <p><b>The tree of words:</b> When you first enter the search engine of S-Din, you could search any word you like, or try selecting a word to explore more! When clicking, You will see the subordinated words. After few repeats, you will finally get the projects that you want. This function is designed to help specify your need, and help you understand your idea better.</p> | | <p><b>The tree of words:</b> When you first enter the search engine of S-Din, you could search any word you like, or try selecting a word to explore more! When clicking, You will see the subordinated words. After few repeats, you will finally get the projects that you want. This function is designed to help specify your need, and help you understand your idea better.</p> |
− | <p><b>Network analysis:</b> This function is designed to help you find out potential relationships between two parts, projects or key words. Sometimes the recommendation may be hard to understand, but perhaps it would open a new direction and lots of inspiration for you.</p> | + | <p><b>Network analysis:</b> This function is designed to help you find out potential relationships between two parts, projects or keywords. Sometimes the recommendation may be hard to understand, but perhaps it would open a new direction and lots of inspiration for you.</p> |
| <p>To learn more about these functions, check <a href="https://2017.igem.org/Team:SYSU-Software/HP/Gold_Integrated">Gold Integrated page</a> for details.</p> | | <p>To learn more about these functions, check <a href="https://2017.igem.org/Team:SYSU-Software/HP/Gold_Integrated">Gold Integrated page</a> for details.</p> |
| </div> | | </div> |
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| <img id="risk-group-img" alt="" class="middle centered" src="https://static.igem.org/mediawiki/2017/f/fe/T--SYSU-Software--safety_risk-group.png"> | | <img id="risk-group-img" alt="" class="middle centered" src="https://static.igem.org/mediawiki/2017/f/fe/T--SYSU-Software--safety_risk-group.png"> |
| <p class="fig-ep">Figure 16: Risk group distribution of parts in S-Din's database.</p> | | <p class="fig-ep">Figure 16: Risk group distribution of parts in S-Din's database.</p> |
− | <p>We checked the parts again to judge if it has "Red Flag" tag. Only 26 parts is tagged. Since we are dedicated to providing an open platform for synthetic biology, the users won’t be limited if they search for ‘Red Flag’ parts; However, users will be warned and advised not to do so once they attempt to design new circuits with ‘Red Flag’ parts.</p> | + | <p>We checked the parts again to judge if it has "Red Flag" tag. Only 26 parts are tagged. Since we are dedicated to providing an open platform for synthetic biology, the users won’t be limited if they search for ‘Red Flag’ parts; However, users will be warned and advised not to do so once they attempt to design new circuits with ‘Red Flag’ parts.</p> |
| <img src="https://static.igem.org/mediawiki/2017/b/b2/T--SYSU-Software--safety_red-flag.png" alt="" class="middle centered"> | | <img src="https://static.igem.org/mediawiki/2017/b/b2/T--SYSU-Software--safety_red-flag.png" alt="" class="middle centered"> |
| <p class="fig-ep">Figure 17: Red Flag part distribution in S-Din's database.</p> | | <p class="fig-ep">Figure 17: Red Flag part distribution in S-Din's database.</p> |
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| <h4>Societal effect assessment</h4> | | <h4>Societal effect assessment</h4> |
| <div class="paragraph"> | | <div class="paragraph"> |
− | <p>Once we had ideas of S-Din, we interviewed professionals or scholars in different fields, and searched related policies. We had a better awareness of our project in the context of scientific inspiration, societal attention, safety and security, and legal considerations.(<a href="https://2017.igem.org/Team:SYSU-Software/HP/Silver">Silver</a> page)</p> | + | <p>Once we had ideas of S-Din, we interviewed professionals or scholars in different fields and searched related policies. We had a better awareness of our project in the context of scientific inspiration, societal attention, safety and security, and legal considerations.(<a href="https://2017.igem.org/Team:SYSU-Software/HP/Silver">Silver</a> page)</p> |
| <p>When S-Din was finished, we introduced it to the professionals. With their advice and help, we wrote a product statement combined with four parts: Terms of use, Bio-safety Alerts, Privacy Policy and Cookie Policy.</p> | | <p>When S-Din was finished, we introduced it to the professionals. With their advice and help, we wrote a product statement combined with four parts: Terms of use, Bio-safety Alerts, Privacy Policy and Cookie Policy.</p> |
| <p>See <a href="https://2017.igem.org/Team:SYSU-Software/Statements" target="_blank">statements page</a> for more details.</p> | | <p>See <a href="https://2017.igem.org/Team:SYSU-Software/Statements" target="_blank">statements page</a> for more details.</p> |
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| <h3>Public promotion</h3> | | <h3>Public promotion</h3> |
| <div class="paragraph"> | | <div class="paragraph"> |
− | <p>When S-Din started to take shape, we promoted it to several iGEM teams and biology laboratories. They were interested in our software and tried out, then we were glad to recieve their encouraging user feedback:</p> | + | <p>When S-Din started to take shape, we promoted it to several iGEM teams and biology laboratories. They were interested in our software and tried out, then we were glad to receive their encouraging user feedback:</p> |
| <p class="quote">"Your database is wonderful! Our project may be more smoothly if cooperated with S-Din!" by Hong_Kong_HKUST</p> | | <p class="quote">"Your database is wonderful! Our project may be more smoothly if cooperated with S-Din!" by Hong_Kong_HKUST</p> |
| <p class="quote">"An integrated software for synbio community." by SCAU-CHINA</p> | | <p class="quote">"An integrated software for synbio community." by SCAU-CHINA</p> |
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| <p class="quote">"More professional articles in database might be better?" by researcher Lin from Prof. Yang Jianhua's Laboratory</p> | | <p class="quote">"More professional articles in database might be better?" by researcher Lin from Prof. Yang Jianhua's Laboratory</p> |
| <img src="https://static.igem.org/mediawiki/2017/b/b0/T--SYSU-Software--hp_figxx.png" class="ui image centered middle"> | | <img src="https://static.igem.org/mediawiki/2017/b/b0/T--SYSU-Software--hp_figxx.png" class="ui image centered middle"> |
− | <p class="fig-ep center">Figure 18: We recommend S-Din to to researchers of LU laboratory.</p> | + | <p class="fig-ep center">Figure 18: We recommend S-Din to researchers of LU laboratory.</p> |
| <p>Ordinary bio-lovers are also interested in S-Din, especially its name. </p> | | <p>Ordinary bio-lovers are also interested in S-Din, especially its name. </p> |
| <p><span class="quote">"The name 'S-Din' is cool! I like it!"</span> by Lin</p> | | <p><span class="quote">"The name 'S-Din' is cool! I like it!"</span> by Lin</p> |
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| <img src="https://static.igem.org/mediawiki/2017/4/45/T--SYSU-Software--hp_figxx2.png" class="ui image centered middle"> | | <img src="https://static.igem.org/mediawiki/2017/4/45/T--SYSU-Software--hp_figxx2.png" class="ui image centered middle"> |
| <p class="fig-ep center">Figure 19: We introduce our product S-Din to ordinary students of SCAU. </p> | | <p class="fig-ep center">Figure 19: We introduce our product S-Din to ordinary students of SCAU. </p> |
− | <p>We are very excited to witness a hit in public when S-Din first met with public. From the original inspiration to the real software product, our software can't be born without continuous communication and timely feedback with public and all related fields. We are deeply impressed by the power of human practices. Although this version of S-Din is not perfect, we'll continue to create a better product. | + | <p>We are very excited to witness a hit in public when S-Din first met with the public. From the original inspiration to the real software product, our software can't be born without continuous communication and timely feedback with public and all related fields. We are deeply impressed by the power of human practices. Although this version of S-Din is not perfect, we'll continue to create a better product. |
| </p> | | </p> |
| <p class="center">Synbio is just a S-din away. </p> | | <p class="center">Synbio is just a S-din away. </p> |