Difference between revisions of "Team:William and Mary/OutreachDatabase"

 
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<div style = 'padding-left: 2%;padding-right: 2%; padding-bottom: 0px;font-size: 25px' ><b>Summary</b></div>
  
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<div style="text-indent: 15px;line-height: 26px;padding-left: 2%; padding-right: 2%;">We aim to expand the infrastructure of sharing and building on past projects in the human practices aspect of iGEM. iGEM has already established such an infrastructure for the scientific research portion of teams’ work to ensure that scientific research is rigorously characterized, accessible, and centralized on the Registry of Standard Biological Parts. We want to help bring some of these same concepts to the Human Practices aspect of iGEM - that is, a strong culture of documentation of activities and their outcomes, and a standard way of characterizing them to facilitate sharing of what has worked and what has presented challenges. We have created a comprehensive database that includes outreach projects done by gold-medal teams in the past two years. The approximately 1,500 entries are in a standardized format that makes it easy to assess and compare projects. Additionally, each entry contains descriptive tags, enabling users to search for specific project categories. We would like to help establish this database as a central part of iGEM. By seeing what has worked well, teams do not need to “re-invent the wheel” and can instead focus on adding improvements. On the other hand, if something did not work well, another team can avoid repeating the mistakes. We feel this will help that iGEM is a continuous force for innovation and progress in outreach. </div>
  
<div style = 'padding-left: 190px; padding-bottom: 20px;font-size: 25px' ><b>Introduction</b></div>
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<div style = 'padding-right: 190px; padding-left: 190px; text-indent: 50px;line-height: 25px;' >Inter-laboratory studies have great implications in both academia research and industry. Comparison of results can not only help determine the characteristics of certain products, but can also validate the test method and determine the source of uncertainty. Synthetic biology aims to achieve predicable gene expression outcomes [1], but challenges for this goal still exist on every level from parts design, circuity complexity to measurement methods. iGEM InterLab study is exactly designed to unravel the source of unpredictability and to quantify the degree of variability [2], the logical of which William and Mary iGEM team shares deeply. We have been an active participator of the InterLab Study since 2015 (the second year William and Mary joined the iGEM family) and we are very honored to be able to continue to contribute this study. </div>
 
  
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<div style = 'padding-left: 10px; padding-bottom: 0px;font-size: 25px' ><b>Introduction</b></div>
  
<div style = 'padding-right: 190px; padding-left: 190px; text-indent: 50px;line-height: 25px;' >This year, the objective of InterLab is to test the precision of gene expression over different RBS devices with a GFP reporter. Teams from around the world are using the standard biological parts, same laboratory bacterium and standardized measurement procedure provided in a detailed protocol. Our team was excited about this year’s project and the improvements that InterLab has made such as the dried down DNA and extra reagents. We started our study on August, 8th.</div>
 
  
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<div style="text-indent: 15px;line-height: 26px;padding-left: 2%; padding-right: 2%;">iGEM has strong infrastructure to ensure that teams can easily share the products of their scientific research with other teams and scientists. The Registry of Standard Biological Parts encourages teams to rigorously characterize projects in a way that makes them replicable, or in a way on which other teams may build. These ideas of replicability and iterative progress are central to the scientific process.</div>
  
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<div style="text-indent: 15px;line-height: 26px;padding-left: 2%; padding-right: 2%;">The iGEM program places a strong emphasis on human practices by having teams reflect upon how their work will impact the world, and how the world can impact their work. Many iGEM teams have created and implemented outstanding human practices projects that they have documented on their wikis. While the expectation exists that human practices projects should be well-documented and an important part of iGEM projects, the infrastructure for outreach does not currently exist in a way that is as standardized or complete as it does for the scientific research. This also means that there is not as much incentive for teams to present their work with enough rigor and detail for others to replicate or build on their outreach projects.</div>
  
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<div style="text-indent: 15px;line-height: 26px;padding-left: 2%; padding-right: 2%;">Our goals in creating the database are the following:</div>
  
  
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<li><div style="text-indent: 5px;line-height: 26px;">Centralize and make more accessible the iGEM outreach projects</div></li>
  
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<li><div style="text-indent: 5px;line-height: 26px;">Present outreach projects in a more standardized way that makes them easier to share and compare</div></li>
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<div style="text-indent: 15px;line-height: 26px;padding-left: 2%; padding-right: 2%;">Our intention with the database entries is not to have a comprehensive explanation of each outreach project. Rather, we want it to act as a basic and standardized description. The team’s  wiki should serve as the more detailed source of information. This is for two reasons. First, teams made their wiki entries themselves and it is the most accurate representation of their outreach projects. Second, database entries are meant to be concise summaries of projects that can be accessed and understood more easily by other teams. We wanted to avoid overcomplicating the database entries by including too much information. Therefore we chose to classify projects by the most important aspects that other teams would want to know if they were potentially interested in building on or using aspects of another team’s Human Practices projects. We include key elements of basic project information, project characteristics, and outcomes.</div>
  
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<div style = 'padding-right: 190px; padding-left: 190px; text-indent: 50px;line-height: 25px;' >We transformed the plasmids (listed below) resuspended from the Distribution Kit into E. coli DH5-alpha cells. Colonies were given 16 hours to grow.</div>
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<div style="text-indent: px;line-height: 26px;padding-left: 7%; padding-right: 7%;"><b>Basic Project Information: </b>This is information that all outreach projects should have. It includes the school name, school section, year, outreach category, and the title of the outreach project.</div>
  
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<div style="text-indent: px;line-height: 26px;padding-left: 7%; padding-right: 7%;"><b>Project Characteristics: </b>Information that is descriptive and could be obtained prior to implementing the project. It documents the aims of the project but does not provide information as to what actually occurred or the outcomes. At the suggestion of Dr. Monica Griffin, the professor in charge of the community-based research and engagement program at the College we included categories considered standard for characterizing communications, education, outreach, and public engagement programs. These include the audience and objectives. The objectives are listed as simple reasons the project was undertaken. Lastly, we also included the “products” produced. Products can be a pdf document, a video, or other tangible material that can be shared and that helps improve the replicability of a project that could be used for other iGEM teams to understand the project and to consider adapting it to their own project.</div>
  
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<div style="text-indent: px;line-height: 26px;padding-left: 7%; padding-right: 7%;"><b>Project Results: </b>Post-project information that helps characterize its efficacy. After consulting with Dr. Griffin about standard outcome information that is used to characterize communication, education, outreach, and public engagement programming we decided to include information in the database on the type of outcome data generated, the reach of the project, and an analysis category. “Data” describes the qualitative or quantitative information used to evaluate the effectiveness of the outreach project on the intended audience. The reach (that is, the number of people reached) gives a metric of the magnitude of impact. Analysis is the team’s own assessment of the outreach events and could include suggestions for improvement.</div>
  
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<div style = 'padding-left: 190px; padding-bottom: 30px;font-size: 20px' >Calibration</div>
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<div style = 'padding-left: 10px; padding-bottom: 0px;font-size: 25px' ><b>Consultation with iGEM HQ to Finalize the Form of the Database</b></div>
  
<div style = 'padding-right: 190px; padding-left: 190px; text-indent: 50px;line-height: 25px;' >Before we started plate reader measurement, we obtained the OD600 reference point and the fluorescein fluorescence curve in the microplate reader to standardize the absorbance reading and cell-based fluorescence reading. Our model was a Synergy H1 Hybrid Multi-Mode Microplate Reader. Ludox-S40 silica nanoparticles were used to calculate the correction factor of OD600. Black 96-well plates with clear bottoms were used. For the plate reader our excitation and emission setting were 485 nm and 528 nm respectively (Same setting was used for all experiments below).</div>
 
  
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<div style="text-indent: 15px;line-height: 26px;padding-left: 2%; padding-right: 2%;">Before proceeding with our database entries, we consulted Todd Kuiken from the Human Practices Executive Committee to learn more about the goals of the committee for improving human practices and to get feedback on our idea of producing the database. Mr. Kuiken told us that for the 2017 year, the committee is trying to make human practices projects more accessible on wikis by having projects on pages with specific links. Additionally, they compiled past exemplary outreach projects for other teams to use to get started on their own outreach. We think the database addresses both of these ideas in a comprehensive way and on an even larger scale; it helps centralize outreach projects and is a resource of iGEM teams to look at past outreach. Mr. Kuiken also talked to us about being more inclusive of Integrated Human Practices projects, as these should be unique between teams, should never be exactly replicated, and cannot be documented in the same way as Education and Public Engagement projects. In order to account of these important considerations, we added the IHP data type to better include data gathered during Integrated Human Practices projects that changed the course of the team’s research.</div>
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<div style = 'padding-right: 190px; padding-left: 190px; text-indent: 50px;line-height: 25px;' >The dilution curve of fluorescein was performed by carrying out a 11-step, 2-fold serial dilution of green fluorescein. Final scaling level was determined from medium-high points in the dilution that is likely to be less impacted by saturation or pipetting error. The μM Fluorescein/a.u.is defined as mean of mid-high level fluorescein concentration divided by the obtained plate reader reading. </div>
 
  
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<div style="text-indent: 15px;line-height: 26px;padding-left: 2%; padding-right: 2%;">Because there is currently no consistent, standardized format for documenting human practices projects, our team entered project data manually. During data entry, we tried to keep wording and information consistent with the information we found in the wikis. We also created project, product, audience, and goal tags based on our judgment of the content of the project wikis. These tags make the database more easily searchable and accessible for future teams. Later, the outreach coordinator edited the database to ensure consistency of the information in the entries.</div>
  
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<div style = 'padding-right: 190px; padding-left: 190px; text-indent: 50px;line-height: 25px;' >2 colonies of each device was inoculated over night into 5 ml Luria- Bertani medium with 25 μg/mL Chloramphenicol in a 37°C, 220 rpm shaking incubator. Cell cultures were diluted to a target OD600 of 0.02 into same LB medium in 50 mL falcon tube covered with foil before use Diluted cultures were further grown at 37°C and 220 rpm. At 0, 2, 4, and 6 hours of incubation, 500 μL aliquot was taken from each two colonies of the 8 devices and were placed immediately on ice to prevent further growth. At the end of sampling point, 4 replicates 100 μl of each sample was pipetted into a 96-well microplate with the arrangement as below. Data was imported into the <a href="https://docs.google.com/spreadsheets/d/1tC-dW10aiqVDURof4HZY8bNCsF5Hvz-XXzgJwrXNu1I/edit#gid=1645629887" style='text-decoration: underline;'> Excel Sheet for submission.</a></div>
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<div style="text-indent: 15px;line-height: 26px;padding-left: 2%; padding-right: 2%;"> The database contains all 1439 outreach projects done by 233 gold medal teams from 2015 and 2016. We finished the database toward the end of our project and found it immensely useful in planning our <a href="https://2017.igem.org/Team:William_and_Mary/Build_Connections" style="text-decoration: underline">Capital Area BioSpace outreach event</a>.</div>
  
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<div style="text-indent: 15px;line-height: 26px;padding-left: 2%; padding-right: 2%;"> <a href="https://2017.igem.org/Team:William_and_Mary/Database" style="text-decoration: underline">Click here to access our Outreach Database!</a></div>
  
 
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<div style = 'padding-left: 190px; padding-bottom: 0px;font-size: 25px' ><b>Results and Discussion</b></div>
 
  
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<div style = 'padding-right: 190px; padding-left: 190px; text-indent: 50px;line-height: 25px;' >Below is the Fluorescein Standard Curve we obtained, from which we can still see the problem of saturation. We also converted the calibrated data of the time-measurement into a uM Fluorescence a.u./ OD600  versus time graph. Besides Device 1 and Device 4, all the others constructs show consistency of standardized fluorescence level in the two colonies over time. </div>
 
  
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<div style = 'padding-left: 10px; padding-bottom: 0px;font-size: 25px' ><b>Findings and Conclusions</b></div>
  
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<div style = 'padding-right: 190px; padding-left: 190px; text-indent: 50px;line-height: 25px;' >From our experiment, we conclude that that BBa_J364100 is a stronger RBS, with an increase of 32.0%, 74.2% and 16.2% expression under J23101, J23106 and J23117 respectively compared to BBa_B0034.</div>
 
  
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<li><div style="text-indent: 5px;line-height: 26px;">Between 2015 and 2016, the average number of outreach projects that gold medal teams undertook rose in all sections - high school, undergraduate, and overgraduate teams. This likely shows an increasing level of attention and effort to do outreach for these teams between these years.</div>
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<div style = 'padding-right: 190px; padding-left: 190px; text-indent: 50px;line-height: 25px;' >The Standardized RBS tested in this experiment, BCD (bicistronic design) 2 is a synthetic cistron leader peptide region that contains two Shine Dalgano sequences that is reported to have increased precise and reliable translation initiation [3]. Device1 and 4, 2 and 5 and Device 3 and 6 features the same strong (J23101), medium (J23106) and weak (J23117) promoters from the well-characterized Anderson promotor family in iGEM registry. Device 1-3 are under standard RBS BBa_B0034, (which William_and_Mary iGEM 2016 has proudly characterized), while Device 4-6 incorporate the test subject BBa_J364100 (BCD2). </div>
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<li><div style="text-indent: 5px;line-height: 26px;">The target audiences remained consistent across years. Below are the percentages of projects targeting each audience. General public was the most commonly targeted audience (36%), followed by primary school students. Much less commonly targeted audiences were vendors, professors, and legislators.</div>
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<div style = 'padding-right: 190px; padding-left: 190px; text-indent: 50px;line-height: 25px;' >Since all of the devices are under constitutive promoters, we assumed that fluorescence expression to be consistent over time in an optimal growth condition (37°C in LB medium). we compiled a total of 48 data of all 4 time points and 2 colonies of the same RBS and did an anova test for BBa_B0034 and BBa_J364100 and obtained a p-value of .085. </div>
 
  
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<li><div style="text-indent: 5px;line-height: 26px;">The information that is available is complete for basic facts and project characteristics, but highly incomplete for outcomes. There was outcome data available for 40% of projects, but information on products produced, reach of the activity, or analysis by the team of the effectiveness of the project was only available for 25%, 12%, and 17% of projects respectively. This makes it difficult to assess the efficacy of past outreach projects and effectively build on them.</div>
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<div style = 'padding-right: 190px; padding-left: 190px; text-indent: 50px;line-height: 25px;' >The failure of getting a significant difference between groups may be due to a small sample size and limitation of place reader measurement. Since Device 1 and Device 4 accounts for most of the variation, and both of which are under the same promoter, another possible explanation would be the context dependent performance of J23101, and an insulator part may be needed to further investigate property of this RBS if the same problem occurs across different teams [4]. We thank the iGEM Measurement Committee again for providing us an excellent opportunity to be part of this study and look forward to see the study results when data from all participating teams are put together.</div>
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<li><div style="text-indent: 5px;line-height: 26px;">The kind of outcome data collected is heavily skewed toward qualitative, for the 40% of projects that do have it. </div>
  
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[1] Kwok, R. (2010). Five hard truths for synthetic biology. Nature, 463(7279), 288-290. doi:10.1038/463288a
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[2] Beal, J., Haddock-Angelli, T., Gershater, M., Mora, K. D., Lizarazo, M., Hollenhorst, J., & Rettberg, R. (2016). Reproducibility of Fluorescent Expression from Engineered Biological Constructs in E. coli. Plos One, 11(3). doi:10.1371/journal.pone.0150182
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[3] Mutalik, V. K., Guimaraes, J. C., Cambray, G., Lam, C., Christoffersen, M. J., Mai, Q., . . . Endy, D. (2013). Precise and reliable gene expression via standard transcription and translation initiation elements. Nature Methods, 10(4), 354-360. doi:10.1038/nmeth.2404
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<div style="text-indent: 15px;line-height: 26px;padding-left: 2%; padding-right: 2%;">The database for 2015 and 2016 teams exists permanently on our wiki, and the Excel file of the database can be downloaded <a href="https://static.igem.org/mediawiki/2017/0/08/T--William_and_Mary--DatabaseSheet.xlsx" style="text-decoration: underline">here</a>. Additionally, teams can update their past projects or submit new projects using <a href="https://docs.google.com/forms/u/1/d/e/1FAIpQLSezaK_FDQgYTln2qBHp-emBAvpQyRmE7vsiq8nuqaCTsDj5tg/viewform?usp=send_form" style="text-decoration: underline">this form.</a></div>
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<div style="text-indent: 15px;line-height: 26px;padding-left: 2%; padding-right: 2%;">We publicized the database and gave the opportunity for 2017 teams to submit projects, but we would like to make this part of the iGEM process -- just as all teams are required to submit a new part to the registry and characterize a new or existing part in the registry, we feel that they should also be required to submit their outreach project to the outreach registry, and characterize it in a standardized way. We want to make it require a low level of maintenance; it took us long time to compile the entire database, but it would only take each team about 20 minutes to submit their own outreach projects.</div>
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<div style="text-indent: 15px;line-height: 26px;padding-left: 2%; padding-right: 2%;">This database format and our findings are meant to help teams think critically about these ideas of replicability, transparency, and accessibility when creating and documenting their outreach projects going forward.</div>
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[4] Davis, J. H., Rubin, A. J., & Sauer, R. T. (2011). Design, construction and characterization of a set of insulated bacterial promoters. Nucleic Acids Research, 39(3), 1131–1141. http://doi.org/10.1093/nar/gkq810
 
  
 
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Latest revision as of 03:16, 15 December 2017




Summary
We aim to expand the infrastructure of sharing and building on past projects in the human practices aspect of iGEM. iGEM has already established such an infrastructure for the scientific research portion of teams’ work to ensure that scientific research is rigorously characterized, accessible, and centralized on the Registry of Standard Biological Parts. We want to help bring some of these same concepts to the Human Practices aspect of iGEM - that is, a strong culture of documentation of activities and their outcomes, and a standard way of characterizing them to facilitate sharing of what has worked and what has presented challenges. We have created a comprehensive database that includes outreach projects done by gold-medal teams in the past two years. The approximately 1,500 entries are in a standardized format that makes it easy to assess and compare projects. Additionally, each entry contains descriptive tags, enabling users to search for specific project categories. We would like to help establish this database as a central part of iGEM. By seeing what has worked well, teams do not need to “re-invent the wheel” and can instead focus on adding improvements. On the other hand, if something did not work well, another team can avoid repeating the mistakes. We feel this will help that iGEM is a continuous force for innovation and progress in outreach.
Introduction
iGEM has strong infrastructure to ensure that teams can easily share the products of their scientific research with other teams and scientists. The Registry of Standard Biological Parts encourages teams to rigorously characterize projects in a way that makes them replicable, or in a way on which other teams may build. These ideas of replicability and iterative progress are central to the scientific process.
The iGEM program places a strong emphasis on human practices by having teams reflect upon how their work will impact the world, and how the world can impact their work. Many iGEM teams have created and implemented outstanding human practices projects that they have documented on their wikis. While the expectation exists that human practices projects should be well-documented and an important part of iGEM projects, the infrastructure for outreach does not currently exist in a way that is as standardized or complete as it does for the scientific research. This also means that there is not as much incentive for teams to present their work with enough rigor and detail for others to replicate or build on their outreach projects.
Our goals in creating the database are the following:
  1. Centralize and make more accessible the iGEM outreach projects
  2. Present outreach projects in a more standardized way that makes them easier to share and compare
  3. Make it easier for future iGEM team to build off past projects and make improvements on existing ideas
  4. Analyze and evaluate recent past outreach and make suggestions for improvement based on the findings
Explanation of the Structure and Content
Our intention with the database entries is not to have a comprehensive explanation of each outreach project. Rather, we want it to act as a basic and standardized description. The team’s wiki should serve as the more detailed source of information. This is for two reasons. First, teams made their wiki entries themselves and it is the most accurate representation of their outreach projects. Second, database entries are meant to be concise summaries of projects that can be accessed and understood more easily by other teams. We wanted to avoid overcomplicating the database entries by including too much information. Therefore we chose to classify projects by the most important aspects that other teams would want to know if they were potentially interested in building on or using aspects of another team’s Human Practices projects. We include key elements of basic project information, project characteristics, and outcomes.
Basic Project Information: This is information that all outreach projects should have. It includes the school name, school section, year, outreach category, and the title of the outreach project.
Project Characteristics: Information that is descriptive and could be obtained prior to implementing the project. It documents the aims of the project but does not provide information as to what actually occurred or the outcomes. At the suggestion of Dr. Monica Griffin, the professor in charge of the community-based research and engagement program at the College we included categories considered standard for characterizing communications, education, outreach, and public engagement programs. These include the audience and objectives. The objectives are listed as simple reasons the project was undertaken. Lastly, we also included the “products” produced. Products can be a pdf document, a video, or other tangible material that can be shared and that helps improve the replicability of a project that could be used for other iGEM teams to understand the project and to consider adapting it to their own project.
Project Results: Post-project information that helps characterize its efficacy. After consulting with Dr. Griffin about standard outcome information that is used to characterize communication, education, outreach, and public engagement programming we decided to include information in the database on the type of outcome data generated, the reach of the project, and an analysis category. “Data” describes the qualitative or quantitative information used to evaluate the effectiveness of the outreach project on the intended audience. The reach (that is, the number of people reached) gives a metric of the magnitude of impact. Analysis is the team’s own assessment of the outreach events and could include suggestions for improvement.
Consultation with iGEM HQ to Finalize the Form of the Database
Before proceeding with our database entries, we consulted Todd Kuiken from the Human Practices Executive Committee to learn more about the goals of the committee for improving human practices and to get feedback on our idea of producing the database. Mr. Kuiken told us that for the 2017 year, the committee is trying to make human practices projects more accessible on wikis by having projects on pages with specific links. Additionally, they compiled past exemplary outreach projects for other teams to use to get started on their own outreach. We think the database addresses both of these ideas in a comprehensive way and on an even larger scale; it helps centralize outreach projects and is a resource of iGEM teams to look at past outreach. Mr. Kuiken also talked to us about being more inclusive of Integrated Human Practices projects, as these should be unique between teams, should never be exactly replicated, and cannot be documented in the same way as Education and Public Engagement projects. In order to account of these important considerations, we added the IHP data type to better include data gathered during Integrated Human Practices projects that changed the course of the team’s research.
Process of Data Entry and Using the Database
Because there is currently no consistent, standardized format for documenting human practices projects, our team entered project data manually. During data entry, we tried to keep wording and information consistent with the information we found in the wikis. We also created project, product, audience, and goal tags based on our judgment of the content of the project wikis. These tags make the database more easily searchable and accessible for future teams. Later, the outreach coordinator edited the database to ensure consistency of the information in the entries.
The database contains all 1439 outreach projects done by 233 gold medal teams from 2015 and 2016. We finished the database toward the end of our project and found it immensely useful in planning our Capital Area BioSpace outreach event.
Findings and Conclusions
  1. Between 2015 and 2016, the average number of outreach projects that gold medal teams undertook rose in all sections - high school, undergraduate, and overgraduate teams. This likely shows an increasing level of attention and effort to do outreach for these teams between these years.
  2. The target audiences remained consistent across years. Below are the percentages of projects targeting each audience. General public was the most commonly targeted audience (36%), followed by primary school students. Much less commonly targeted audiences were vendors, professors, and legislators.
  3. The information that is available is complete for basic facts and project characteristics, but highly incomplete for outcomes. There was outcome data available for 40% of projects, but information on products produced, reach of the activity, or analysis by the team of the effectiveness of the project was only available for 25%, 12%, and 17% of projects respectively. This makes it difficult to assess the efficacy of past outreach projects and effectively build on them.
  4. The kind of outcome data collected is heavily skewed toward qualitative, for the 40% of projects that do have it.
Recommendations for the Future
The database for 2015 and 2016 teams exists permanently on our wiki, and the Excel file of the database can be downloaded here. Additionally, teams can update their past projects or submit new projects using this form.
We publicized the database and gave the opportunity for 2017 teams to submit projects, but we would like to make this part of the iGEM process -- just as all teams are required to submit a new part to the registry and characterize a new or existing part in the registry, we feel that they should also be required to submit their outreach project to the outreach registry, and characterize it in a standardized way. We want to make it require a low level of maintenance; it took us long time to compile the entire database, but it would only take each team about 20 minutes to submit their own outreach projects.
This database format and our findings are meant to help teams think critically about these ideas of replicability, transparency, and accessibility when creating and documenting their outreach projects going forward.