Weekly Reports
Week One
Our first week was all about diving deep into the project literature and getting a solid understanding of what we're getting into. We kicked things off by immersing ourselves in the world of olfactometers – what they are, how they're built, and what makes them tick. Alongside that, we delved into head-fixation systems for mice, figured out the ins and outs of water delivery while they're fixed in place, and got to grips with pumping air into our olfactometer. And let's not forget about getting acquainted with the basics of Arduino. Plus, we had the opportunity to check out the Python code from the 2023 BioFabLab project and even gave their olfactometer a test drive. As if that wasn't enough, we also managed to squeeze in a visit to a 3D printing workshop at Université Paris Cité – definitely a packed schedule!
Monday, 05.02.2024: We started our week with a meeting with Maëlle, our PhD student extraordinaire. She gave us the grand tour of the olfactometer and shared some insights from last year's project. Once we wrapped that up, it was time to get organized, so we whipped up a Gantt Chart to keep us on track and dived into the bibliography of the 2023 BioFabLab group that paved the way with their olfactometer project.
Tuesday, 13.02.2024: This was our deep dive into the Python code powering the olfactometer. But before we could get started, we had to make sure Anaconda and GitHub were all set up and ready to go. Things hit a snag when one of the commands didn't want to play ball, so we had to roll back our Anaconda Python version to 3.7, which did the trick. During our testing, we noticed the solenoid valves heating up faster than expected, so we made a note of it to tackle later.
Wednesday, 14.02.2024: Today was all about hitting the books. Each of us took on one of the main topics – Jelena tackled the Arduino setup, Erin dived into water delivery and mouse licking tracking, while Martha took charge of the head-fixation system. After a day of research, we regrouped in the afternoon to share our findings and brainstorm next steps.
Thursday, 15.02.2024 : Another day, another meeting with Maëlle to iron out any wrinkles in our understanding. We put our heads together to brainstorm ways to lower the pressure in the air tank and sketched out a rough draft of a head-fixation setup. We also stumbled upon something called a lickometer, which seemed like a game-changer for water delivery and tracking mouse behavior. Wrapping up the day, we compiled all our research and ideas into a presentation for our supervisor.
Friday, 16.02.2024: TGIF! We took a break from the books and headed off to a 3D printing class on campus. It was a hands-on session where we got to grips with Fusion 360 and tried our hand at both 2D and 3D designs. A nice change of pace to round off the week in Saint-Germain des Près!
Week Two
Moving into our second week, our focus remained on key objectives: establishing our Tiki Wiki website and populating it with our comprehensive literature review and project presentation. Additionally, we needed to allocate time for a mandatory security training session for the lab. Within the scope of our project, our primary tasks revolved around finalizing the setup for the olfactometer components, refining our designs, and developing a detailed cost estimation.
Monday, 12.02.2024:Commencing the week with a concerted effort, we embarked on setting up our Tiki Wiki accounts and convened with Maelle for a thorough discussion. This meeting served as a platform to consolidate our findings and insights from the preceding week, facilitating strategic planning for the upcoming phases of our project.
Tuesday, 13.02.2024: Commencing the week with a concerted effort, we embarked on setting up our Tiki Wiki accounts and convened with Maelle for a thorough discussion. This meeting served as a platform to consolidate our findings and insights from the preceding week, facilitating strategic planning for the upcoming phases of our project.
Wednesday, 14.02.2024: With a divide-and-conquer approach, we distributed responsibilities among the team members. Jelena took charge of establishing our Tiki Wiki website infrastructure, while Erin delved into curating our literature review and Martha dedicated her efforts to finalizing the intricate 3D design of our head-bar for the fixation system.
Thursday, 15.02.2024: Amidst ongoing website development, we actively participated in the weekly journal club session organized by the Vetere lab. Following an engaging discussion on pertinent research papers, we convened with our supervisor to provide a comprehensive update on our project trajectory. Recognizing the need for precision, it was unanimously decided to conduct measurements on the mice subjects to optimize the design parameters of the head-bar and overall experimental setup.
Friday, 16.02.2024: The day marked a pivotal moment as we finally had the opportunity to interface with our experimental subjects – the mice. Conducting meticulous measurements, we gained invaluable insights that necessitated adjustments to the head-bar design, including the incorporation of a protective cap. Subsequently, we transported the olfactometer to an Arduino class, leveraging every available opportunity to advance our project goals, while dedicating additional time to website refinement before concluding the week's activities.
Week Three
Entering into the third week of our project, our primary objectives revolve around the fabrication of prototypes based on our designs and the subsequent refinement of these designs. Concurrently, our aim is to procure all necessary components essential for the assembly of the new olfactometer.
Monday, 12.02.2024:
As customary, we commenced the week by initializing our tasks with the opening of our Tiki Wiki accounts, followed by a collaborative meeting with Maelle. During this session, we engaged in a comprehensive review of our findings and brainstormed potential ideas stemming from the insights gathered during the initial week. Subsequently, we delineated a strategic plan outlining the subsequent steps required to propel our project forward.
Tuesday, 13.02.2024:
With a concerted effort, our team members embarked on individual tasks aligned with our overarching objectives. Jelena spearheaded the setup of our Tiki Wiki website, while Erin delved into the depths of our literature review. Concurrently, Martha focused on the meticulous finalization of the 3D design for the head-bar integral to our fixation system.
Wednesday, 14.02.2024:
Advancing into the implementation phase, we commenced the 3D printing process for the initial iteration of our head-bar design. In parallel, efforts were dedicated to the ongoing refinement of our website writeup and the enhancement of its design aesthetics.
Thursday, 15.02.2024:
Continuing our efforts, we diligently progressed with the refinement of our website content and structure before engaging in the Vetere lab's weekly journal club session. Following a stimulating discourse centered around significant research papers, we convened with our supervisor to provide an extensive update on our project's progress and present our evolving ideas. It was unanimously agreed upon to proceed with taking precise measurements of the mice subjects to facilitate necessary adjustments to the head-bar design and the broader experimental setup.
Friday, 16.02.2024:{HTML} A significant milestone was reached as we had our first encounter with the mice subjects, conducting meticulous measurements crucial for design optimization. Identifying areas for improvement, particularly in the head-bar design, we determined the inclusion of a protective cap as a necessary modification. Subsequently, we transported the olfactometer to an Arduino class, utilizing every available opportunity to advance our project goals, while concurrently dedicating additional time to the ongoing refinement of our website.
Week Four
Diving into week four, our main mission is to get all the necessary parts ordered up so we can hit the ground running with building the olfactometer come next week. Plus, we're finally buckling down to set up our Tiki Wiki Website and sprucing up the user interface of our olfactometer control program by tweaking the view.py file.
Monday, 26.02.2024: Erin wrapped up the cost estimation sheet, and we lined up a meeting for the next day to hash out the details with Maelle and Gisella. We made the call to stick with the original valves to keep costs in check and decided to get creative with a plastic sheet to mold into a cone shape. Unfortunately, the 3D printers were on the fritz again, so our plans to print prototypes of the head-fix apparatus and the final olfactometer box design hit a snag.
Tuesday, 27.02.2024: Kicking off with a meeting with Maelle, we dove into the nitty-gritty of the cost estimation and made the call to get quotes on all the items ASAP. Then, we swung by the metalwork facility at the ESPCI, where they offered to whip up a resin model of our head-fix apparatus before crafting the final design from metal. Erin got to work finding quotes for all our needed items while Jelena tackled the Tiki Wiki website, and Martha worked her coding magic to streamline the view.py file, making it run smooth without any pyfirmata module headaches.
Wednesday, 28.02.2024: Time to divide and conquer. Martha duked it out with the view.py code, wrestling with those pesky indentation errors. Meanwhile, Erin kept plugging away at the website, and Jelena brainstormed ideas for controlling water release, sketching out potential Arduino setups.
Thursday, 29.02.2024: Brainstorming session alert! We huddled up to draft a setup for tracking mouse licking using an Arduino, brainstorming ways to adjust water flow based on the released odor. Armed with these ideas, we dove into writing code to control the water valve, aiming to seamlessly integrate it into our existing setup. Oh, and of course, we didn't forget about our Tiki Wiki website – that's still very much in progress.
Friday, 01.03.2024: We kept plugging away at the Tiki Wiki website, even adding a slick homepage to spice things up. Attempting to tweak the User Interface was a bit of a struggle, but we'll crack that nut eventually. Wrapping up the week, we met with Gisella and Maelle to show off our progress and discuss next steps. Turns out, we need to get all the tubes and materials to build the olfactometer, so we finalized the quotes and shot them off to Maelle. Let's keep this momentum going!
Week Five
As we embark on the fifth week of our project, our objectives stand firm: to navigate a crucial session with the Makerlab and bring the circuitry and components assembly for the olfactometer to fruition. With eager anticipation for the arrival of our ordered items, we're poised to initiate the construction phase without delay.
Monday, 04.03.2024: With determination in our hearts, Erin and Jelena joined forces to inject new life into the Tiki Wiki platform, embarking on a journey of development and refinement. Meanwhile, Martha immersed herself in the intricate world of graphical user interface (GUI) codes, diligently fine-tuning each element to perfection. The day was a testament to our collaborative spirit, as each team member poured their expertise into their respective tasks, driving tangible progress forward.
Tuesday, 05.03.2024: Our rendezvous with the Maker Lab proved to be a catalyst for innovation and strategic planning. Opting for a streamlined approach, we resolved to utilize a single Arduino at 7V to oversee water release and valve control, complemented by the adoption of LP7346 MOSFET modules for enhanced functionality. In our quest to ensure mouse-friendly operation, we embarked on insulating components and integrating novel features such as a voltage divider, LDR light-dependent resistor for heightened visual feedback, and a capacity sensor to facilitate seamless mouse interaction. Armed with meticulous plans, we eagerly prepared to put our designs to the test, leveraging a diverse array of tools including relays, a Maker Lab soldering board, Arduino, wires, and tubes to propel our project forward.
Wednesday, 06.03.2024: With a blueprint in hand, we plunged headfirst into the practical execution of our plans. Drawing upon our collective expertise, we meticulously crafted the circuitry, establishing crucial connections and delving into the nuances of analog-to-digital integration. Meanwhile, Jelena and Erin assumed responsibility for soldering the Arduino setup, ensuring each connection was made with precision, while Martha devoted her efforts to perfecting the GUI code. The day was characterized by a harmonious blend of hands-on craftsmanship and coding finesse, as we took significant strides towards realizing our project vision.
Thursday, 07.03.2024: With our roles clearly defined, we set out to tackle the day's objectives with unwavering determination. Erin diligently tied up loose ends in the ordering process, meticulously verifying that all necessary items were secured, while also dedicating herself to the refinement of our Tiki Wiki website. Meanwhile, Jelena undertook the intricate task of soldering all cables for the new olfactometer setup's circuitry, ensuring each connection was executed flawlessly. Simultaneously, Martha poured her expertise into fine-tuning the GUI codes, striving for a seamless user experience. In a collaborative display of ingenuity, Erin and Martha embarked on a creative endeavor, fashioning odor delivery cones by ingeniously modifying falcon tubes—meticulously sawing off their bottoms and skillfully drilling and grinding holes into them. The day was a testament to our unwavering commitment to excellence, as we meticulously fine-tuned each element of our project to perfection.
Friday, 08.03.2024: As the week drew to a close, we persisted in our efforts to refine the Tiki Wiki website, infusing it with newfound vitality with the addition of a captivating homepage. Despite encountering challenges in our attempts to tweak the User Interface, our resolve remained unwavering as we continued to explore avenues for improvement. In the afternoon, we convened with Gisella and Maelle to present our progress, showcasing the fruits of our labor and engaging in insightful discussions about the path forward. Assessing our needs for tubes and materials essential for constructing the olfactometer, we realized the necessity to procure everything anew. With meticulous attention to detail, we finalized the quotes and swiftly dispatched them to Maelle, setting the stage for the next phase of our journey with unwavering determination and enthusiasm.
Week Six
In Week 6, our primary objectives centered around finalizing all codings, including the Graphical User Interface (GUI), and initiating the assembly of the olfactometer upon the arrival of our necessary items. Additionally, we aimed to 3D print a prototype of the olfactometer box to expedite the assembly process.
Monday, 11.03.2024: We continued with the work form last week. Jelena conducted extensive testing on the water release system, confirming the functionality of our lickometer setup even when exposed to water. Erin, in collaboration with our supervisor, finalized pending orders and redesigned the olfactometer box for 3D printing. However, our plans hit a snag when the 3D printers in the open lab were found to be non-functional. Undeterred, we promptly reached out to the MakerLab, exploring alternative avenues for printing our box. Meanwhile, Martha successfully completed the codes for the GUI, bringing us one step closer to seamless integration with the olfactometer. The arrival of one of our orders signaled a promising start to the week, setting the stage for the upcoming assembly process.
Tuesday, 12.03.2024: Tuesday brought a sense of anticipation as we eagerly collected our first order, heralding the commencement of our assembly preparations. Following this, we returned to the Saint-Pères campus, where Jelena and Erin focused on testing the water delivery system and constructing a prototype water bottle compatible with the system. Concurrently, Jelena meticulously planned the circuitry, laying the groundwork for seamless integration into the olfactometer. Meanwhile, Martha and Erin dedicated their efforts to Tiki Wiki, ensuring comprehensive documentation and data backup procedures were in place, further streamlining our project management processes.
Wednesday, 13.03.2024: Wednesday commenced with our scheduled meeting with Gisella, where we discussed project progress and addressed any emerging challenges. Additionally, we participated in the lab meeting, where Clement presented his ongoing research, fostering knowledge exchange and collaboration within the team. Throughout the day, we continued to enhance our Tiki Wiki platform, ensuring all project-related information was meticulously organized and accessible. Concurrently, we devoted time to refining the water setup, troubleshooting any issues encountered, and eagerly awaited the arrival of our soldering set to further advance our assembly preparations.
Thursday, 14.03.2024: Thursday was marked by hands-on practical work as we embarked on soldering connections on the soldering board, a crucial step in our assembly process. Simultaneously, we maintained our focus on updating and refining Tiki Wiki, ensuring all team members were abreast of the latest developments. Additionally, we made progress in setting up the water valve system, further solidifying our foundation for the olfactometer assembly.
Friday, 15.03.2024: Friday saw us continue our endeavors remotely, as we dedicated time to further enhancing Tiki Wiki and finalizing the layout for our project poster. Despite our proactive efforts, we found ourselves still awaiting the arrival of essential components, underscoring the importance of patience and adaptability in project management.
As the week drew to a close, we remained steadfast in our commitment to achieving our objectives, leveraging effective communication and collaboration to navigate challenges and make steady progress towards our goals.
Week Seven
In Week 7, our primary focus remained on achieving key project milestones, namely the completion of the olfactometer, finalization of Tikiwiki tasks, and the initiation of our poster draft. We aimed to advance the construction of the olfactometer, a pivotal component of our project. This involved assembling various components, testing functionality, and ensuring precise calibration for accurate results. Moreover, we were committed to wrapping up outstanding tasks on Tikiwiki, our collaborative platform for project documentation and coordination. Finally, we aimed to lay the groundwork for our project poster, crafting a preliminary draft to outline our research, methodologies, and anticipated outcomes.
Monday, 18.03.2024: We kicked off with a burst of productivity as we obtained the necessary transistors and swiftly began soldering cables to them. Simultaneously, our creative juices flowed as we delved into crafting a draft for our project poster, ensuring it captured the essence of our work. Additionally, we took the opportunity to update the Tikiwiki platform, ensuring our progress was accurately documented for all to see.
Tuesday, 19.03.2024: Tuesday marked a crucial phase in our project progression as we delved into the meticulous testing of transistors, pivotal components of our olfactometer assembly. With meticulous attention to detail, we assessed the functionality and reliability of each transistor, ensuring they met our stringent quality standards. Concurrently, our focus shifted back to Tikiwiki, where we dedicated ourselves to refining the layout of our poster draft. Collaborating closely, we strived to create a visually compelling and informative presentation of our project, aiming to captivate and engage our audience effectively. Despite the technical complexities and creative challenges encountered, our team remained steadfast in our pursuit of excellence, laying a solid foundation for the tasks ahead.
Wednesday, 20.03.2024: Midweek brought excitement as the olfactometer box arrived, marking a significant step forward in our project's physical construction. With the transistors successfully tested and deemed operational, our focus shifted back to completing the remaining tasks on Tikiwiki. Meanwhile, we embarked on the meticulous process of preparing the olfactometer box, carefully cutting and sanding plastic board pieces to ensure a precise fit.
Thursday, 21.03.2024: Thursday was a day of meticulous planning and coordination as we laid out the valve and tube connections for the olfactometer, ensuring everything was positioned correctly for optimal functionality. Simultaneously, we attended to journal work and participated in a productive lab meeting, pooling our collective insights and ideas. The day concluded with a brief yet essential photo session to document our progress and achievements thus far.
Friday, 22.03.2024: As the week drew to a close on Friday, our efforts culminated in the assembly of the olfactometer. With precision and care, we drilled holes into plastic sheets and expertly glued them together, ensuring a sturdy and airtight construction. Additionally, we meticulously attached tubes to valves, sealed openings with hot glue, and affixed vial holders to both sides of the olfactometer. Anticipating future needs, we preemptively drilled holes for potential extensions, demonstrating foresight and strategic planning in our project development.
With the olfactometer assembled and our Tikiwiki tasks nearing completion, we stand on the brink of realizing our project objectives. As we reflect on the week's accomplishments, we are energized and motivated to push forward, confident in our ability to deliver a successful outcome.
Week Eight
In the final week of the BioFabLab project, our objectives were twofold: to finalize tasks on Tiki Wiki and complete the assembly of the olfactometer while ensuring it underwent successful testing. Our aim was to submit the completed olfactometer by Wednesday, with contingency plans in place to troubleshoot any issues that arose. Additionally, we aimed to wrap up our project poster and produce the remaining video tutorials, providing comprehensive documentation for future reference.
Monday, 25.03.2024: Monday was a day marked by perseverance and triumph as we tackled challenges head-on in pursuit of our objectives. Despite encountering numerous obstacles during the wiring and Arduino integration into the olfactometer, we remained undeterred, overcoming each hurdle with determination and resilience. Through innovative problem-solving, we added additional super glued pieces to stabilize the positioning of the Arduino and breadboard, ensuring optimal functionality. Furthermore, we meticulously incorporated transistors into the assembly, constructing an additional plate and drilling holes to secure their positions with cable ties. Amidst these technical endeavors, we successfully concluded our work on Tiki Wiki and finalized the development of our project poster, setting a solid foundation for the week ahead.
Tuesday, 28.03.2024: Tuesday saw us delve into the intricacies of olfactometer testing and documentation, as we embarked on a series of critical tasks. With meticulous attention to detail, we isolated and elongated the capacity sensor cable, ensuring precise functionality during testing. Concurrently, we rigorously tested the water valve, filming comprehensive video tutorials for olfactometer box assembly and water valve setup. These tutorials were promptly uploaded to Tiki Wiki, enriching our project documentation and facilitating future replication of our work. However, despite our best efforts, we encountered challenges during the olfactometer test run, prompting adjustments to our code. In response, we sought assistance from the maker lab to address the issue, demonstrating proactive problem-solving and collaboration. Additionally, we expanded the accessibility of our project by sharing the STL files for the head-fixing apparatus on a public drive and linking them to Tiki Wiki. As the day drew to a close, we added the link to our olfactometer GitHub repository, further enhancing the accessibility of our project resources.
Wednesday, 27.03.2024: Wednesday was characterized by significant milestones as we continued to make strides towards project completion. With a steadfast focus on the poster, we refined its layout and incorporated graphical representations to enhance clarity and visual appeal. Concurrently, we proudly showcased the olfactometer to the lab, delivering an extensive introduction on its functionality and features. Providing a comprehensive overview of our project's evolution, we outlined past developments and potential future improvements, ensuring a thorough understanding among our peers. Additionally, we meticulously organized and restocked all materials utilized from the open lab, ensuring a seamless transition for future projects.
Thursday, 28.03.2024: Thursday was dedicated to fine-tuning our project poster, as we made final adjustments to layouts and prioritized the creation of graphical representations. With a keen eye for detail, we endeavored to present our research findings in a visually compelling and informative manner, ensuring maximum impact and engagement.
Friday, 29.03.2024: As the week drew to a close, Friday heralded the completion of our project poster, marking a significant achievement in our journey. With all elements finalized, we conducted thorough reviews and made any necessary final touches, ensuring the poster was polished and ready for submission. Reflecting on the week's accomplishments, we were pleased with the progress made and the effectiveness of our time and project management strategies. Despite facing various constraints, our team demonstrated resilience and adaptability, ultimately delivering a successful outcome. With the poster completed, we looked forward to the upcoming submission date, confident in the quality of our work and the impact it would make.