Team:IISER-Tirupati India/Excellence
It is often said that excellence is not just an act, it's an attitude. An attitude that is inculcated with rigorous efforts of making the world a better place.
The potential to bring a positive change in the world is synonymous with synthetic biology and we all agree with that fact. Thus, we must make the world a better place by taking concrete actions to include everyone in science and its solutions.
The team of IISER-Tiruapti_India believes that excellence can only be achieved in the realm of synthetic biology when everyone has access to its tools and technologies and when its solutions are aimed at the betterment of everyone irrespective of their gender/sex and abilities/disabilities.
We wanted to increase access to synthetic biology to scholars from all backgrounds and thus, we began the change at home - from our very own labs and the scientific literature we use. .
LAB EYES
BACKGROUND
Around the world, many students face difficulty in the fields of Science due to visual impairment. Many theoretical resources have been made available for legally blind or visually impaired individuals. The Braille system of writing has been developing at a rapid pace and being used in assistive technologies to connect visually impaired and blind people with the rest of the world. But when it comes to lab accessibility, very limited progress has been made to make the lab space more accessible to people with visual impairments.
Assistive technology is an umbrella term covering the systems and services related to the delivery of assistive products and services. Assistive products maintain or improve an individual’s functioning and independence and thereby promote their well-being. Such assistive technologies and products are extremely helpful for disabled people.
A synthetic biology laboratory typically uses a lot of instruments that require specific calibration and those calibrations more often than not require visual aid to find and then choose the correct consumable. When it comes to chemicals, again, the different chemicals are identified by reading their names printed on them. These ways of identification are extremely difficult or even impossible for visually impaired and blind individuals.
Usually, visually impaired or blind individuals will resort to touching, tasting, or smelling the consumables or chemicals to identify them on their own. But in a synthetic biology laboratory, most of the consumables need to be in a sterile condition, and chemicals cannot be touched/tasted/inhaled due to potential toxicity. Other than that, many instruments have similar shapes and sizes and one cannot solely rely on touch to make sure they are using the correct instrument to the correct calibration.
As we can guess, the aforementioned problems make it extremely difficult for people with visual impairments or blindness to work in the laboratory independently and efficiently.
However, being visually impaired doesn't in any way hamper the ability of the individual to analyze scientific results, understand the concepts or even write research papers [1]. We wanted to come up with a solution to this problem faced by low vision and blind researchers/students in the synthetic biology laboratory.
Through our iGEM 2021 project, we were able to come with an easy-to-use solution.
THE SOFTWARE
We wanted to explore the possibility of making assistive technology software for synthetic biology laboratories that can help the students/researchers recognize the different consumables and chemicals without visual aid that can be replicated anywhere in the world.
To execute our idea, our team collaborated with Ms. Agrima Sawhney and Mr. Mohit Kumar Pradhan who are 3rd-year CSE and EEE undergraduates from Inderprastha Engineering College, Uttar Pradesh, India.
Thus, we came up with LAB EYES - a laboratory assistive technology software for low vision and blind individuals. This software can scan QR codes and convert them to speech.
QR codes are unique, universal, and cost-effective to identify anything that we see all around us. We used this unique technology of generating QR to make a more inclusive laboratory environment for all. A QR code can be generated concerning anything and it will provide a unique identity to that.
Moreover, a QR code can be easily scanned using any device with a working camera and can work anywhere. This is a great boon for technologies around the world and we wanted to explore the possibility of making it a great boon for laboratory accessibility.
DESKTOP APP
LAB EYES started with a vision to develop an offline desktop app for static computers in laboratories. This app can be downloaded on any computer or laptop and will be fully functional for devices having a working camera, speaker, and mic. This app is developed so that it can be used in areas even without a stable internet connection. It was also developed keeping in mind the safety of the user and data generated from this app. The data generated from this app will be completely offline and will be saved on the respective device only.
The app has special inbuilt keyboard commands for its different features to further assist its usage without visual aid. The user just needs to point the substance towards the camera of the desktop computer to find out what it is.
The app has two main features:-
- GENERATE QR CODE :
- SCAN QR CODE :
The app can generate a unique QR code for the different consumables and chemicals of the laboratories, and these QR codes will be saved offline on the user’s device. The user can generate any number of QR codes using this feature by typing the relevant words. The QR codes can be generated for the specific calibration of the instrument. They can further be printed in different sizes and then pasted on the respective instruments and chemicals.
The app also has the feature to scan QR codes that are generated and then convert them to speech. This feature will allow the user to know what the particular consumable/chemical is. This way, they can know specifically the calibration of the instrument and specifically identify the chemicals we are using.
WEBSITE
This website was specially designed to be accessible to anyone around the world and laboratories that don't have a static computer.
The website has been developed keeping in mind the mobility and independence of the user, while the desktop app has been developed keeping in mind the performance of the software.
This website can also be accessed through the user’s phone/tablet/ laptop anywhere in the world. The website has the same features as the desktop app, it will be able to access your device's camera and microphone to perform the same functions via the internet.
This website will further enhance the user’s independence, as it can be a mobile device and taken directly to the chemical/consumable rather than bringing the chemical/consumable to the person.
Link to judging release
Link to GitHub Repo
QR CODE LIBRARY
In addition to making the software, we have generated the QR codes of the most commonly used chemicals and consumables in a synthetic biology laboratory using our software. These QR codes have been compiled into a QR code library that is available for download to future iGEM teams and any synthetic biology lab at large.
This QR code library will give iGEM teams a heads up in making their synthetic biology laboratories more inclusive and welcoming towards visually impaired and blind individuals.
Future iGEM teams can directly download the library of QR codes, print the relevant QR codes, and paste them on the respective consumables and chemicals.
Future iGEM teams can also update the QR code library by simply adding the new QR codes they generated throughout their iGEM journey. This will aid in creating a more expansive list of chemicals and consumables for future reference.
In addition to that, we have also provided instructions on how to use the QR codes in a lab setting to get the optimum efficiency from the LAB EYES software.
QR code library -
Instruction manual for LAB EYES is
LIMITATIONS
While developing any assistive technology software, certain limitations need to be taken into consideration. Some of the limitations with the LAB EYES software are:-
- Due to the COVID-19 restrictions, we were not able to open our laboratory doors to visually impaired and blind individuals. Thus, we could not get feedback on how well LAB EYES performs in making the laboratory accessible to the community.
- The desktop application will only work on the Windows OS. Due to recent updates in permission, the mobile version of the LAB EYES website faces trouble working on iOS devices. Our team will work on improving this in the future.
- The speed and accuracy of the scanning process depend highly on the resolution of the camera device.
- Being a text-to-speech software, there can be differences in the accent of the words spoken by the software. This can hamper the understanding of the user as the same word can sound different in different accents. This can lead to confusion on the part of the user. Our team will try to introduce a function of switching AI voices in the software in later versions of this software.
- This app uses the “English” language as the medium of communication and the names of the chemical or consumables are spoken in the English language. This can make it difficult for people to understand speech, especially those whose primary language is not English.
FUTURE ASPECTS
Our assistive technology software LAB EYES has a lot of potential for further development. For instance, it can easily be put together with hardware that will not require any external device on the user’s part like a mobile phone or a laptop to scan the QR code and convert it to speech.
A more expansive list of the QR code library can be sent to the companies in charge of manufacturing and packaging the consumables and chemicals required for a synthetic biology laboratory. These QR codes can then be printed directly on the respective chemicals and consumables. This will save resources on part of the teams and labs, in general, to make their laboratory more accessible.
DOCUMENTING RESEARCH WITH TRANSGENDER AND INTERSEX INDIVIDUALS
BACKGROUND
While working on the inclusivity aspect of our project, we went over resources to find the correct scientific literature to back our claims and understand more about the different intersex and trans conditions. Scouring through scientific databases and finding the relevant literature can be challenging, especially when the research in an area is scarce and there are multiple publications of the same paper. We firmly believe that synthetic biology has the potential to solve real-world problems that are faced by everyone. In most cases, the term “everyone” is not able to include individuals belonging to gender-diverse communities.
Most of the projects and research in synthetic biology have been built keeping in mind the gender binary and proposed solutions that can only cater to the needs of the gender binary. One of the reasons could be a lack of awareness and the other one could lack resources to find the relevant scientific literature regarding their project. This ultimately leads to the exclusion of people from general solutions like the transgender and intersex communities.
DATABASE
To bridge the gap between synthetic biology researchers and the relevant scientific literature, we decided to make a database solely focussing on research around transgender and intersex communities.
This database was made using the free software EPPI-Reviewer Version: 4.12.3.0. This software allows researchers to import items from different databases and then analyze them, sort them according to different search strings and then export the data.
For this particular database, we searched the PubMed and PsychInfo databases for finding the different scientific literature published regarding the Transgender and Intersex communities.
The search strings for the initial searches were broad terms like transgender, non-binary, gender dysphoria, Congenital Adrenal Hyperplasia, Turner Syndrome, and many more such as intersex conditions. These search strings resulted in a total of 51,682 scientific research papers.
After scanning for duplicates, a total of 4,615 research papers were deleted based on having a similarity index between (0.9600- 0.9900) giving the final database of 47,067 papers that were based on transgender and intersex individuals.
However, generating the data was not enough, we took our search to the next level and started sorting the different literature according to the most common areas of research in Synthetic Biology. Our searches were inspired by the broad topics addressed in iGEM projects such as microbiome, diabetes, reproductive health, surgeries, and many more. To make the references received more credible, we obtained those research papers that had both terms in the title and abstract of the paper.
Example: The search for “transgender” and “microbiome” in the title and abstract yielded 3 references. Now researchers in synthetic biology, who are working with the human microbiome can look for resources in those 3 papers and make their project more inclusive towards the transgender communities.
Similar searches were run with the different intersex conditions. This database can also give a more holistic view of the different intersex conditions and the transgender spectrum and even highlight areas that need more research.
Along with the scientific literature, we have also given a short description of the different conditions. This will further enhance the understanding of researchers of that particular condition and they can then assess if that condition is relevant to their research area or not.
The results of different search strings have been documented showing the Year of publication, PubMed ID, short title, and Title of the research paper.
This database has been documented in a way that other people can build upon it and can add more research papers to it as when the research is documented.
LIMITATIONS
Certain limiting factors exist in regards to the database:-
- It can help synthetic biology researchers find the relevant literature on open-access databases like PubMed and PsychInfo. This is not inclusive of scientific literature available on different databases that are not open access.
- The scientific literature presented in this database is up to October 2021.
- The scientific literature presented in the database is not sorted according to the different sub-topics of relevance, but only covers the broad research areas. This can make it difficult to sort through the extensive literature for some areas.
- As there is no review performed on the papers as of yet, it can be possible that some papers that are just remotely related to the research areas are also present. There can also be duplicates within the different search strings for the same condition. For example, there may be duplicate papers within the search strings of “transgender, metabolism” and “transgender, diabetes”
We feel that this database is a step in the right direction in knowing more about how transgender and intersex individuals have been depicted in scientific literature and build on those solutions using synthetic biology as a tool to pave way for more inclusive solutions.
FUTURE ASPECTS
Evidence maps are an emerging research method to “collate, describe, and catalog” knowledge across a broad field of study. This information can then be leveraged by stakeholders to inform policy and clinical decision-making. Using this database, an evidence map can be made for research-based trans and intersex communities. Such an evidence map and its open access will be extremely useful for policymakers, researchers, clinicians, and even the stakeholders to know more about the field and make informed decisions based on it [2] .
References:-
- Sahtout, N. (2020). How science should support researchers with visual impairments. Nature.
- Marshall, Z., Welch, V., Minichiello, A., Swab, M., Brunger, F., & Kaposy, C. (2019). Documenting research with transgender, nonbinary, and other gender diverse (trans) individuals and communities: introducing the global trans research evidence map. Transgender health, 4(1), 68-80.
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