Team:Athens/Integrated
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- People
MEDEA/HP ΜΕΔΕΑ
Integrated Human Practices
accessibility
noun [ U ] US /əkˌses.əˈbɪl.ə.t̬i/
the fact of being able to be reached or obtained easily
the quality of being easy to understandOverview
Since the first steps of our team and our brainstorming sessions, accessibility has been a key concept that inspired many important decisions and plans of ours. First and foremost, it determined our final decision on which project to work on; unlike the other project ideas we had, we found really exciting the fact that the aptamers project could give us the chance to approach this exciting field from our own perspective and, why not, revolutionize it! Since then, we have set some clear goals for our project; apart from creating something innovative, we have worked to design an alternative method for identifying new aptamers, which will be essentially more simple, easier to use and more reasonable in terms of man-hours and cost than the existing options.
What’s more, the process of realizing how we, as a students’ initiative, can contribute to the communication of Science, has been quite enlightening! Synthetic Biology, specifically, is still little-known in Greece; there is no reference to the field in school, little or no representation in most related academic curricula, while there are few SynBio researchers whose - very significant - work is often poorly diffused to the academic community and the public. These are some crucial facts that inspired us, since the beginning, to reach out and interact with other people. Read more about our public engagement here.
To sum up, our team, as part of its Integrated Human Practices, explored many different ways to incorporate accessibility as a fundamental component to our project:
Accessibility for scientists and researchers
Creating a “smart” and “independent” system
In our pursuit of a method substantially more accessible for other scientists, but also better in terms of results, we focused early on on creating something radically new, rather than a variation of the existing method, SELEX. In order for scientists of different fields, backgrounds and expertise to be able to use our method in a meaningful way for their research, we were convinced that what we needed was a “smart”, dynamic biological system that would require only basic input and simple operations from its user. Inspired by the 2018 Nobel prize in Chemistry, we decided to incorporate directed evolution as the basic mechanism that would provide us with the desired aptamers in a “smart”, self-sustainable way. While intensively reviewing the available literature, we came across a pioneering phage-assisted continuous evolution system for proteins, called PACE! We, therefore, contacted Dr. Ahmed Badran of the Broad Institute of MIT and Harvard, who, during his Ph.D. research in the group of Professor David R. Liu at Harvard University, participated in the development of the PACE system. Dr. Badran gave us invaluable feedback on our design and, what’s more, he propose we look up a CRISPR-assisted directed evolution system developed by S. O. Halperin et. al, called EvolvR. This contribution of Dr. Badran’ s turned out crucial for our project; the EvolvR system satisfied all major desirable characteristics and we eventually switched for this, solving major design issues we faced with the PACE system as past of our project!
Nevertheless, it would be an omission of ours not to talk about the people who played an important role during our brainstorming period, helping us in deciding on our final project. One of these people was Dr. Marianna H. Antonelou, Ph.D., Assistant Professor of Animal Cell Biology at the National & Kapodistrian University of Athens (NKUA). We contacted Dr. Antonelou at that time as we were seriously thinking of developing a kind of “synthetic hemoglobin” with SynBio. In our meeting with Dr. Antonelou, a specialist on hemoglobin, we discussed the major challenges of this project idea. “Blood is as complicated as the human brain”, she commented characteristically, and she was one of the reasons we let go of the hemoglobin project (at least for now ;) ).
CHEAT-E & Morbidostat - an easier way to get results
Besides our main project, our hardware and measurement endeavors were inspired by our pursuit for something accessible. On the one hand, we came up with a novel method for CHeap Experimental Assessment of Terminator Efficiency (CHEAT-E!). While most commonly used ways to evaluate terminators’ efficiency involve measuring the relative expression of fluorescent proteins, such as GFP, RFP or YFP, usually with FACS technology, we proudly propose an alternative approach that does not involve the use of special machinery or technology and can, therefore, be applied by anyone with basic lab skills. Read more about our CHEAT-E method on our Measurement page!
On the other hand, we designed and assembled a DIY morbidostat that supports a monitored bacterial culture, while maintaining constant bacterial populations and directed evolution pressures. This is, in terms of setup, components and overall cost, the simplest way to get a functional setup! In our Hardware page, we have, also, included detailed instructions, photos and a video where one can watch the morbidostat’ s assembly process step by step! We believe these resources can be very helpful for scientists in need of a bacterial culture arrangement, which can now be obtained much more easily!
Safety first, iGEMer second...
Safety is key; if it's not safe, it can't be employed by everyone. We strived to make sure all major aspects of our project do not pose any possible danger for scientists and the world. We revised and edited our circuit's design multiple times, until we had a system, whose functional units are controllable. Additionally, at first, we wanted to use a neurotoxin produced by a cone snail species as the target molecule for our proof-of-concept. However, after discussing about this with Dr. Piers Millett, vice president of Safety and Security at the iGEM Foundation, as well as Professor Stathopoulos from the University of Patras, Greece, we decided to opt for a simpler and safer target molecule, as is CRP! Finally, we created a Safety Checklist and we wish for it to serve as a handy, readily available tool for any scientist to assess whether he/she work with Safety! Read more on our Safety page!
Asking Advice from the Experts - the Center for Open Science
While looking for resources that could help us with our Human Practices, we came across a site; osf.io. OSF is a free, open platform to support research and enable collaboration, by making data, materials and other resources readily available and accessible. We emailed the Center with no further delay and we were pleased to receive an answer from Alex DeHaven, one of OSF's collaborators! Alex offered concise advice on how to improve the accessibility of our work. More specifically, he strongly suggested we be as precise, clear and analytical when documenting our work. This is, undoubtedly, necessary in order for other scientists to reproduce or build on our work and, for this reason, we tried our best to be thorough in every step and every endeavor; project design, wet lab methods, software, hardware, modeling and, ultimately, the creation of this Wiki page!
The more, the merrier - The iGEM Aptamers Hub
Our main collaboration proposal to our fellow iGEM teams had to do with creating an Aptamers Hub, that is, a platform for all iGEM teams working with aptamers to interact, discuss problems, find solutions, inspire and find inspiration in others’ projects! We embarked on this journey as we were highly motivated to find a way to make aptamers research more accessible to us and to others by connecting people whose interaction can be mutually beneficial. Read more about the Aptamers Hub and our vision for it on our Collaborations page!
Accessibility to Science
Popularizing Synthetic Biology in Greece
Accessible means reachable, but also intelligible. Synthetic Biology, let alone iGEM teams, is still a new and widely unknown thing in Greece. For our efforts to have true and long term value, we set as our priority to spread the word about what we do and its great potential! Besides, all our interviewees pointed out the importance of getting out of the lab and sharing your achievements with your community! In this context, we planned out carefully a series of Ηuman Practices that allowed us to approach many different people; at the Athens Science Festival we interacted with people of all age groups and backgrounds, at the 2019 UNIque Days we addressed last-year high school students trying to figure out which academic path to follow, at the Scientific Congress of Hellenic Medical Students we presented Synthetic Biology to a passionate crowd of fellow students and young scientists, who, tomorrow, will lead in the biomedical field, while, at the event we held at the NTUA, we reached out to students of engineering faculties. What's more, as Alex DeHaven from the OSF | Center for Open Science advized us, we tried to set clear goals about what concepts, information and ideas we want to communicate to people.
Besides connecting with people through events, we sought to benefit from the power of traditional communication media and social media. We were honored to see articles about our team being published in the Greek newspaper “TA NEA” and the electronic newspaper “Athens Voice”, two of the largest newspapers in Greece in order of circulation! What’s more, with the help of Dr. Konstantinos Vavitsas, prominent SynBio researcher who we also interviewed, we managed to publish an articleabout our work on the EUSynBioS blog, the online platform of the European Association of Synthetic Biology Students and Postdocs!
As for our presence on social media, we put a great deal of effort in setting up and managing our accounts and we are more than pleased that we managed to attract more than 3.000 followers, with whom we shared every step of progress and every special moment throughout the last months!
Accessible to everyone
Our work would be of less importance if it wasn’t accessible to everyone. We have committed ourselves to creating a wiki page that is agreeable for all users, regardless of disabilities and conditions that may affect the way they use and perceive it. There is a wide range of impairments that can act on one’s online experience, but we can generally distinguish the following main categories:
| Vision | This includes a partial or total inability to see or to perceive color contrasts.
| Hearing | Some users have a reduced ability to hear.
| Motor skills | These are people with difficulty moving parts of their bodies, including making precise movements (such as when using a mouse).
| Photosensitive seizures | Conditions such as epilepsy can cause seizures that are often triggered by flashing lights.
| Cognitive disabilities | There are also many conditions that affect cognitive ability, such as dementia and dyslexia.
Below you will find a list of the things we took into consideration. As you will realize yourself, these are some pretty simple and straightforward design tips, yet they can make a huge difference! We encourage all iGEM teams to follow them!
1. Make sure your site is keyboard-friendly (tab key)
2. Be concise. Use simple, straightforward language in the active voice and try to avoid excessive content. When people using assistive technologies (A.T.) (e.g. screen readers) were asked, 67% of them said that crowded websites with too much text was the biggest website issue they face. If, however, you're putting a lot of text onto your website, break it into smaller paragraphs.
3. Use headers to structure your content correctly. The heading structure is often used as a shortcut way of navigating a page.
4. Put periods in abbreviations (e.g. F.B.I.)
5. Consider the balance of text, graphics, and animations on your web page and include a clear method for users to hide animations.
6. Keep your tables as simple as you can. Avoid using tables for anything but tabular data.
7. Make sure that any colorful graphs, charts, and infographics also display numbers and values so that users can process the information more easily.
8. Use alt tags on images: all uploaded documents to your website should be available in a text format, not just a PDF or other image-based format that can’t be understood by screen reading tools. Careful: ensure the alt-tag is used properly so those who use A.T. can understand what a given link might actually do if activated.
9. Create subtitles and transcripts.
10. Ensure that your text can resize up to 200% without losing information. As for the font size, try to avoid absolute units, such as specifying text size using pixels. Instead, use relative sizes, which enable the text to scale depending on other content and screen size. You should also never turn off user scalability as this will make it difficult for users to resize the text at all.
11. Avoid Automatic Media and Navigation. It’s also best to avoid automatic navigation, such as carousels and sliders. This can be incredibly frustrating if the viewer needs more time to absorb all the information before moving on to the next slide or section.
12. Give the clickable item a wider range so the user can click on it within the item's general area.
13. Be careful of how you use color, of color combinations and contrast. In fact, color highlights make the information more accessible to users who can see the color difference. For those who cannot, you can still use color to reinforce information, as long as color is not the only way this status is presented.
14. If you've done your best to make your site disability-friendly, include a section that lays out all of the ways your site is accessible. Alternatively, you can post a guide on tips and tricks users can implement on their own computers.