Team:Vilnius-Lithuania/Human Practices
Human Practices Overview
To See A Society
Encouraged by the rapid Life Sciences development in Lithuania and our team’s previous achievements, we decided that it was meaningful to share our experience with the younger generation. Visiting schools, inviting pupils to visit Vilnius University Life Sciences Center and introducing SynDrop to them helped us not only to reveal but also clarify our own attitude towards synthetic biology. The discussion that we have organised during the DNA Day’s celebration has become a great inspiration to search for a creative approach to implement our project’s idea and to make it more public-friendly.
Passing on the Knowledge to the Younger Generation
Excited by the possibilities synthetic biology has to offer, our team aimed to involve younger generation in this novel field of science by educating them in schools, during pupil-olympiads, and meetings of other societies.
Our team members continued the tradition of previous Vilnius-Lithuania iGEM teams and held lectures for students in different schools across the country. During these visits scholars had an opportunity to learn the main principles of synthetic biology and laboratory work bearing in mind SynDrop project as an example. Also, high-school students have visited our laboratory in Vilnius University Life Sciences Center and implemented their knowledge into practice, e.g. learning how to balance a centrifuge or using Burker camera in order to calculate cells.
Additionally, we delegated our member Valentas to represent our team in organising the 51st LitBO (Lithuanian Biology Olympiad) and its bootcamp where students were preparing for the International Biology Olympiad. He was responsible for giving lectures about fundamental biological principles and synthetic biology, as well as planning experiments for students.
Our instructor Auksė held a lecture for Turing School students (13-18 yrs. of age) who planned to become future inventors and leaders of the IT sector. She delineated the possibilities of synthetic biology, revealed future applications of CRISPR/Cas system, and most importantly described ways of how IT skills could be applied in bioinformatics and above mentioned fields.
DNA Day's Celebration
Looking for new ideas and methods to educate school children and hear their thoughts on synthetic biology and our project, we found a spectacular occasion in the calendar. Our team organised an event marking the 65th anniversary of the day in 1953 when James Watson and Francis Crick published paper in Nature about the structure of DNA. There could not have been a better occasion to teach scholars about synthetic cells and gene expression in non-cellular systems. Additionally, this day was never celebrated in Vilnius University Life Sciences Center before, thus our team settled to launch a new continuous tradition.
The main attraction of the DNA Day was a number of interactive activities designed for curious schoolchildren of various Lithuanian schools. All activities introduced the main idea and concepts of our project as well as the Life Sciences Center itself as a place where significant research happens. Schoolchildren visited several departments of this Center: Department of Biochemistry and Molecular Biology, Department of Botany and Genetics, Department of Eukaryote Gene Engineering, Department of Bioinformatics, Sector of Microtechnologies, Department of Immunology and Cell Biology and Department of Protein-DNA Interactions. At first glance, Life Sciences Center looks a bit like a labyrinth, so in order to make this Day more fun and interesting for students, we set up orienteering competition. Through interactive activities we revealed why it was important to visit the abovemention departments, and how they were related to developing our project’s idea. Pupils were given some tasks and their answers led them to next points in another departments.
First of all, after speaking about laboratory safety rules and showing equipment which included pipetmans, centrifugal machine, thermocycler and other, we explained the central dogma of molecular biology. Pupils learned about several methods we use while carrying out experiments. For example, they were able to try dilution while doing it with some colorful solutions and measuring the exact solution’s concentration with a spectrophotometer.
During other activities schoolchildren had to identify particular restriction sites of DNA sequence relying on activity of given restriction enzymes. It helped pupils to learn about making recombinant DNA which is used to transfer information.
In the Sector of Microtechnologies participants got to know how proteins are inserted into synthesised liposomes. We explained our project’s main idea to pupils and how it might be used in such fields as genetics or molecular biology.
Schoolchildren enjoyed spending a day in our research centre very much and were really interested in solving our biological puzzles. Quoting pupils: “this way it was easier to solidify the gained knowledge”. Later all attendees of the DNA Day were invited to a science communication lecture #DNAtoDo held by professor R. Meškys, our former PI. Professor had presented the latest technology and innovations in the field of life sciences and pointed their impact on our everyday life. Relating this lecture to the purpose of the celebration, he introduced not only traditional DNA, but also XNA (synthetic, Xeno DNA) and its possible future applications.
The final part of DNA Day’s celebration was a coaching-type discussion about the provisional steps in turning our dreams into ideas and those ideas into real world applications. We invited some of the Vilnius-Lithuania iGEM 2018 stakeholders and partners to initiate a dialogue between them, the representatives of our team, and the community of Life Sciences Center. During the discussion, possibilities and most common difficulties which young scientists face while trying to implement their ideas in a university or by launching startups were covered. Considering that more and more teams set up their own companies after iGEM, we suggested an idea of developing our project into a possible startup. We learned that stakeholders were impressed by our project, however some concerns regarding complexity and time consumption were put into light. During the discussion an idea was suggested for us to develop a software which would ease the implementation of our project goals and would also be useful for other scientists in the field.
To sum up, celebration of the DNA Day allowed schoolchildren to take a glance at the project we have created for this year’s competition. It was a pleasure to see how enthusiastically pupils enjoyed the orienteering competition and how inspired they were after understanding our projects’ aim and significance. Even though it was kind of an entertainment for schoolchildren, we also felt encouraged to consider our project in all its bearings and find more creative ways to improve it. In addition Vilnius-Lithuania team members had a great opportunity to take a different look at the subjects they studied and pass their knowledge to the new generation. The discussion not only gave us information about startup-possibilities, but also inspired us to consider setting up one ourselves - we became sure about the necessity of our project and gained insights on how we could improve it.
Finally, we hope that the DNA Day’s celebration will become a pleasant yearly tradition in Vilnius University Life Sciences Center.
Link to our leaflet of DNA dayBioHackathon
Discussions with the stakeholders we had during the DNA Day celebration was a great inspiration to search for a creative approach to implement our idea and to make this year’s project more public-friendly. Representing various professional-fields, the participants of the discussion proved us that a multidisciplinary team nowadays is a key to success. This is why we decided to organize an event for people who face difficulties and lack a multidisciplinary team when trying to implement their scientific ideas.
We dedicated the first weekend of August to the international coding competition - “BioHackathon: Lab Issues”. It was the first event of this type ever to be held in Lithuania. We considered that BioHackathon would be a great opportunity for representing life sciences to people from various fields and age groups as well as an opportunity to work together in order to expand and boost our project.
Because symbiosis between Life Sciences and IT fields in Lithuania still is in its initial stage, prior to the BioHackathon we prepared a short cycle of lectures. Prospective BioHackathon competitors have attended Prof. V. Ašeris’, P. Gibas’ (PhD) and K. Leonavičius’ (PhD) lectures during which they introduced main concepts of biology to the IT specialists and fundamentals of coding and IT projects for people from the Life Sciences field.
The general idea of hackathons is for a team to create any minimum viable product during the 48 hours of coding. During our BioHackathon, each team including ours, had a specific goal: to create wet-lab-applicable projects in order to reduce the burden of commonly complicated or simply time-wasting daily laboratory tasks.
Seven teams from Lithuania and three iGEM teams from Sweden (iGEM team Lund), Finland (iGEM team Aalto-Helsinki), and Netherlands (iGEM team Groningen) have participated in our BioHackathon. We invited the Minister of Economy of the Republic of Lithuania Mr Virginijus Sinkevičius to welcome the participants and open our coding games. During the opening speech he has emphasised that future is not separately in IT or Life Sciences fields, but rather in their fusion. Neuroscientist Dr. Urtė Neniškytė held a lecture about brain efficiency improvement, Co-Founder and CEO at “Integrated Optics” Evaldas Pabrėža gave a lecture named “Long Haul Start-ups. Motivation Not to Fail” which were productive and short distractions from coding. Throughout the BioHackathon thirteen IT and Life Sciences mentors have kindly consulted and guided all teams.
BioHackathon was also a breakthrough for our software part of the project. As we mentioned in the DNA Day page, event’s final discussion proved to us that we needed to develop a software which would ease the implementation of our project goals and would also be useful for other scientists in the field. Notably, our this year’s project is extremely complex and time-consuming. Not only experiments, but also preparation for them requires outstanding precision. One of the examples of such preparations is coating of microfluidic devices. Efficient coating is not only a challenge that we faced, but rather a common limitation in microfluidic’s work. Thus previous discussion and the appropriate setting of the BioHackathon encouraged us to create LipoVision - a software tool for precise device-coating. 48 hours of coding and consultations with mentors proficient in visual recognition, laid the foundations of our software which was finished considerably shortly after the BioHackathon. It helped us save a great amount of time and what is even more impressive - LipoVision is currently being tested in our research centre, Microfluidic’s lab.
Not only did the integrated human practices help us come up with a software for our project, but also helped other iGEM and BioHackathon teams to create tools and programmes, that we and they could apply in daily laboratory work. After BioHackathon, we have spent more than a month upgrading LipoVision and only then we were able to use this tool in our daily practice. Team iGEM Lund created a search-engine which made online navigation among iGEM projects easier and immensely simplified finding of necessary BioBricks. It undoubtedly helped us a lot while doing the analysis about available and unavailable BioBricks for our project. Team „Skrebulai“ has designed a computerized system for visual recognition and analysis of DNA electrophoresis and SDS-PAGE gels. We immediately applied this tool because it demonstrated great potential to help save time. Due to all these reasons we strongly believe that these inventions will easily find many users not only among iGEMers, but also students and scientists all around different laboratories.
Even though our BioHackathon was the very first Life Sciences Hackathon organised in Lithuania, a lively interest in this event became a perfect evidence that there was a great demand for more events of this type in Lithuania.
Open Source Applications
Due to the fact that programmes and tools were created in order to reduce the burden of scientists’ manual work, we share some open source applications for the iGEM community to use.
ChromAutoGrapher"Kristina"
ChromAutoGrapher Team „VCS Practice“ has designed an application which automatically processes documents including the data of high performance liquid chromatography (HPLC). This application automatically generates standardised protocols for given HPLC assays by converting selected files from pdf to text format, as well as calculating Average value, Standard Deviation and Covariation (COV).Data labelling game
While creating this application, an idea of designing a game was chosen intentionally by team BPTI_import_TeamName. Scientists (“gamers”) can choose to open, for example, blood sample images and analyse blood cells there. As a result, the more certain findings they label there, the higher level is reached in this game. Also, all information about labelled findings is saved and used in order to enable the programme identify them itself. VPTIBuffy the Bufferbot
Team Groningen designed operating system for Buffy - the buffer robot which is used while preparing solutions and reduction of pH value. This Bufferbot is able to keep track of buffer’s pH and reach the desired value avoiding human-made errors. Buffy
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