Abstract ED

  • Grad Life: The Usual Beginning of Term Issues

    I’ve been prompted to discuss some of the recent issues I’ve been having. There’s been a slight delay on some issues popping up, but as projects rise and fall, changes to my computer set up are required. Also I just moved. Again. We’re now counting 9 moves since I’ve started graduate studies. Let’s chat.

    Projects and Pathing

    What feels like a common silly thing to wrestle with which each new code package is the installation of specific dependencies and setting up folders and paths in a particular fashion to allow the use of said new fancy code package. Without going into detail, I’m astonished that I was able to follow some specific set of instructions to install GDAL (notorious for being tricky to set up since a number of dependencies need to be upgraded and downgraded at various steps in the installation). However, I’m at a loss when it comes to the more cryptic error messages (Figs. 1 and 2).

    Usually what I do is Google and check various forums for days on end, find some workaround and install something completely different instead. This time it’s looking like I really might have to figure out the issue. On a related note, speaking with my labmates did help out for another software problem I was having. Thank you!

    Figure 1. A screenshot of Anaconda. I cracked open my “clusters” environment and got a series of messages that I have no recollection of setting up. Here I was just trying to reproduce the weird error that I get when I try to import a python package! More to solve I suppose. I should start documenting what I do to set up my environments.
    Figure 2. The actual issue. The log has nothing useful in it by the way.

    Housing

    Wow, what a problem. This is a nation-wide issue of course. There’s the actual cost of housing that means I get to spend something like 80% of my income and have 20% leftover for groceries and any sort of enjoyment in life outside of work, then there’s bad housing. Let’s document my housing experiences briefly.

    Location zero: never even moved in. I got a last minute notification that the place I had originally planned was not going to work out.

    Location one: Landlord insisted on meeting up in a different city. Played games with the offer (stating there was another tenant they preferred). Entered premises without notice. Did not resolve issues. Gave me keys to everyone’s bedroom and asked me to keep it a secret (I refused) because they didn’t have a property manager and didn’t want to drive in to unlock the doors for people. Refused to address the issue of a surprise pet someone had been hiding in their room (and causing allergic reactions) despite this being a condo with no pet rules. Failing to notify the condo association of the tenants and associated vehicle licenses. Gaslighting and yelling. It goes on.

    Location two: Landlord lived in the house. When viewing the place, they indicated that kitchen and pool were for common use. Linens were provided. Moved in. Got yelled at for cooking and having “food scents”. Insisted that people in the past just ate take out every day. Threatened to call the police on me. Put something questionable in my room that caused it to smell. Lied about the passcode for the entrance. I didn’t even last the two weeks I had paid for.

    Location three: Just a crash pad at a friend’s place while avoiding Location two and figuring out where to go.

    Location four: Perfectly fine! The place was a little small and out of the way. This was a non-issue until the pandemic rolled around and I was stuck indoors all the time due to a wasp problem in the backyard.

    Location five: Pretty great. Minus the extreme heat (no AC) and roommates that had weird sleeping hours that resulted in a lot of stomping overhead. The folks were great, but the random footsteps overhead really got to me after a while. I was all set for the rest of my degree. Until I wasn’t.

    Location six: Turns out it’s really hard to find housing when the university suddenly declares in person classes again. After 60+ calls and messages, and several in person visits where people were making offers on the spot, I finally found a place reasonably priced and close enough to bus. Only issue is that the landlord hated onions. Okay. I could deal with that for a bit.

    It turns out that it was a lot more than that. There was a lot of random sudden sniffs outside my door, and loud music being played all the time from upstairs, and a lot of guests (guess what we weren’t allowed to have?). The heat would also get randomly turned off and she demanded our windows be opened for hours to air out. Eventually me and my law school roommate decided to look into the legality of our living conditions and decided that we were indeed protected by the Residential Tenancies Act and our lease was nonsense. Over the holidays our landlord someone developed some terrible illness wherein her doctor insisted that no scented things were allowed in the house. Of course, they felt welcome to inspect our quarters. Somehow my roommate spilled an entire bottle of perfume that the landlord didn’t notice, but my diffuser that had water in it for over a month was a problem. No wonder I didn’t submit my thesis in time to work from home the next term.

    Location seven: Great! Lovely roommate, reasonably nice location. Wasps in the house and mice in the walls. Can’t win ’em all. Those issues never got resolved properly. There was also incredibly poor heat distribution in the house and a gap in our entry door, so we often had a space heater on. Oh, and the house down the street was regularly broken into and we had a couple fires in the five months I was there. I wouldn’t have enjoyed living there much longer.

    Location eight (skipping over living from home and living at a remote campsite for three weeks): Okay. Housing in Toronto is rough. A family friend let me stay for a bit while I was waiting on residence to let me in. It was a lot of being treated like a surrogate daughter though. Not the most comfortable, but alright.

    Location nine: Finally! I have arrived! I applied way back when I received my original acceptance and followed up after the response date had passed. I was on the wait list. Cool. Then I got in and picked a date. Great! I emailed closer to the move in date asking where the lease was. I was informed it was in the works. It showed up in my inbox a week before move-in with some additional information. For example, there was a link that informed me I would receive a move-in time via email and I should confirm this worked for me. The email never arrived despite reaching out several times and getting a response for elevator booking on the Friday before move-in. No one seems to work on the weekends.

    Move-in day. I waited until around 10 that morning, calling in several times to see if I could get a hold of someone. I even got transferred once. To no avail. Anyhow, I show up and it’s all good. Then I get into the apartment. Fairly quickly, I notice it is not all good. There are several issues with the apartment, most of which are cleanliness and electrical related. I have a quick chat with the office that gave me keys, and they assure me that I can submit a maintenance request and most issues will be addressed between 24 and 48 hours.

    Surprise! I am unable to fill out the maintenance form. To that point, I am also unable to complete the arrival inventory (where I can state the condition of things where I found them). I email IT and someone fixes this a day later citing a mysterious issue and I have now have access. Alright then. I fill out the form and make 3 specific maintenance requests, and within a day, I see notice that my requests have been updated and are in various stages of progress. I come back after going to a workshop out of town and see a notice indicating that one request is a non-issue, and another has been confirmed as an issue. A nice little notice informs me that they will be coming back. Cleanliness issues have not been addressed.

    A week passes, and I check with the front desk how to escalate. They are surprised to hear that my issue is ongoing. I follow the information I was given to reach out to another group to figure out what has been going on. Another 48+ hours passes, and I hear nothing. I email again, requesting an update. 48+ hours go by. Nothing.

    This morning, I ask the front desk to escalate. They are surprised to see me again, and apologize once more, this time promising to reach out to the custodial staff directly. I come back mid-day to address my rumbling stomach, and find my door open and people inside my apartment. Weird. Someone just emailed me confirming they would come by tomorrow morning to take photos. After extensive discussion and several phone calls (from the staff in my apartment), I am assured that their superiors have contracted someone to come by tomorrow. We shall see if this happens. It is evident that there are some communication issues within the Maintenance group themselves. At first, no one was addressing my issue. Now there are at least 4 other people involved. Apparently people had been trying to knock on my door for the last 2 days instead of simply emailing me back.

    Lessons (RE)Learned

    Being a student with limited financial resources can be rough. No doubt about it. I spoke with a few others who had been living in residence and they made it clear that they had ongoing issues that had never been resolved or required escalating several times and external intervention to address. I have absolutely paid my way out of bad housing situations in the past, but this isn’t a viable solution for everyone all the time. Being persistent in resolving issues is the only way they move forward, and it takes more time than I would like to spend. It would be wonderful if the people I had to interact with were competent, especially when I am reliant on them or pay for a service. To quote roughly the individual I spoke with the first time around regarding cleanliness, “It’s because they’re part-timers. I don’t get it. They should work hard until they’re full-time, then they can slack off on the job.” Admittedly, I bit my tongue when I heard that from what appeared to be one of the full-time staff. I think I may have responded with, “Right, so 24-48 hours?”

    Pile of Projects, Solutions?

    I’d love to be able to compartmentalize my life so that I can focus on one thing at a time. Research, TA duties, housing, a semblance of financial security, and my personal life. It doesn’t quite work out that way though. So instead, I write myself a small to-do list for each “project” in my life and see how much bandwidth I have that day or week. This doesn’t always work out (I still have what is hopefully an hour long task to wrap up a short project), but it seems to help. I will eventually find some time to work on my pet projects, such as in Figure 3. Electroforming and shampoo making, here I come!

    Figure 3. Not all is bad. I finally picked up an LED lamp that mimics part of the spectrum necessary for happy plant growth. It also provides a warm light instead of the fluorescents everywhere else in the apartment!
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  • Grad Life: Stuck at Home During a Conference

    My last post discussed catching COVID-19 and all the fun I had with the resulting data that came about it. What I didn’t cover was the conference I was attending remotely during the bulk of the time I was sick. At first, I was supposed to attend the 54th DPS (Division for Planetary Sciences) meeting in person. Alas, this was not possible after contracting a very contagious virus. Instead, I found myself prepping to check in online and make the best of it. Here are some of the tips that I developed when I was getting ready for another conference online (AGU). An alternate version of these tips can be found on the PVL blog (http://york-pvl.blogspot.com/).

    Tips for attending a scientific conference (when you’re remotely at a hybrid event):

    1. Identify your favourite conference snacks and drinks
    2. Purchase, make, or make student-budget friendly versions of said snacks and drinks
    3. Plan chores that require at most 1 hour of your time. Preferably a bunch of 10-15 minute chores
    4. Acquire bluetooth headphones
    5. Identify some clothes for dressing up (or down)
    6. Pick a few “key” sessions you want to be awake for and some interesting ones to pad out the rest of your time
    7. Chat with your lab mates on your preferred communication method of choice.

    Let’s break these down a bit. Say you were really looking forward to attending the conference in person and had already planned for those days to be away. However, you’ve fallen sick or some event has taken place that prevents you from attending. You might as well try to get part of the conference experience at home! While there will be significantly less mingling with others and networking opportunities will be at most, awkward and stilted, you can still delight in the little snack breaks while reflecting on the state of the field.

    This brings us to tip number 1. If you’ve been to a conference before, what snacks did you enjoy during the breaks? Personally I like that there are usually several tea options, and sometimes the coffee is palatable. The previous conference I had attended online (planned), I had the time to order some coffee samples and pick up a variety of snacks from the asian supermarket. This time I was stuck in quarantine, so I made sure I had a kettle and a massive stock of tea bags. This covers tip number 2 as well. It doesn’t have to be fancy, but having the ability to make hot drinks on demand is quite nice. It’s reminiscent of downing drinks to soothe your throat in the dry, conference room air.

    Since I had to attend the conference online rather last minute, I wasn’t able to grab a photo of all the cute snacks and drinks that I had during this time. I will say that my favourite snack was a soft matcha flavoured cake. My favourite drink was lavender tea, freshly plucked from the front yard when my folks could remember to grab some for me, since I was functionally under house arrest.

    Lavender from my folks. This + honey made my sore throat much better. Herbal tea (infusion if you’re picky) is a nice alternative to the gallons of coffee I usually imbibe.

    Tip number 3 and 4 involve keeping yourself busy. Unlike an in-person conference, there are very few things you can look at that you are unfamiliar with. You likely won’t have access to the attendees (no camera facing that way, zoom only shows the speakers) so figuring out who else is at that session is out unless they speak up during Q&A. Instead, you could be getting some mundane tasks done! I personally can’t look at a screen continuously, so laundry, cleaning the kitchen, organizing bookshelves, watering/trimming plants, etc. all give me breaks away from the screen, but I’m not doing anything so critical that I can’t check what’s on the screen if it’s particularly important. Tip 4 gives you the flexibility to move around without fear of wires tangling or blasting the audio (less of an issue if you don’t have roommates, but still a nice option). Earphones are also an option, but I find headphones to be a bit better with universal fitting. Also, you now have the wonderful ability to choose to go to the bathroom while still listening to the sessions.

    It’s all good to be perfectly cozy while stuck at home (or if you’re so inclined, going outside while still plugged into the conference). A big part of the conference experience is being present though. For me, that means dressing in a slightly snappier manner than I normally might. Regardless, I would want to have a change of pace for “conference time”, much like when working from home, it’s helpful for me to dress up for “work hours”. Dressing down could be a fun alternative to this though. After all, no one can see that you’re in the goofiest of onesies. Similarly, no one will know (other than your housemates) that you attended in a full ballgown and mask. So that’s tip 5.

    Tip 6 is applicable to any conference you attend. There is only so much time in a day, so pick your favourite events to go to. Figure out what’s relevant to your interests. Not much more to say about this one. Tip 7 is similarly applicable always. Should you find yourself longing for some company, or wanting to experience the social aspect of the conference, checking in with your lab mates or anyone else at the conference can be nice. If you’re all together (remote or in person), it can be nice to schedule some hangout time outside of the planned events.

    Lastly, it’s always a good idea to tap out whenever you’re feeling tired. No point attending a conference in your brain is on the fritz. Return to your comfy couch, or pop back into that hotel room as need be. Enjoy your next conference!

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  • Sketchy Science: A Study on (personal) COVID-19 Rapid Test Results

    Welcome to my first post! Here I tell you about one of the silly things that I get up to when I’m sick and don’t quite have the capacity to focus on regular work.

    Disclaimer: I am by no means a medical professional. No advice is being offered in this article. This article is intended to be humorous and demonstrate some basic techniques to pull data from images.

    Acknowledgements: My family for taking me in when I was feeling unwell and insisting I eat well during the bout of COVID I got. They also got extra tests for me when I wanted to be consistent about the materials I was using for this study.

    Materials and Methods: COVID-10 Rapid Tests (Rapid Response Diagnostics, Rapid Response (R) COVID-19 Antigen Rapid Test Cassette for At Home use) retrieved from various Shopper’s Drug Mart pharmacy sections. 11 samples were taken. 2 blanks were discarded following calibration. Samples were taken every 24 hours with up to 5 hours difference from the 7 pm ET reference time. Figure 1 demonstrates the contents of each box of tests.

    Figure 1. Back of the Rapid Response (R) COVID-19 Antigen Rapid Test Cassette. Image provides brief description of the purpose of the contents and an illustration of the contents of the kit. Included are 5 test cassettes, swabs, extraction buffer tubes, and waste bags. Instructions for Use are also included.

    To create the sample, the provided swab was inserted into the right nostril until the swab encountered the back of the nose and swirled several times to collect mucosal liquid. The same swab was applied to the left nostril in the same manner. The collected fluid on the swab was then swirled into the pre-packaged test vial. The test vials (buffer extraction tubes) in all cases were vials with a foil seal, retaining the buffer. The buffer soaked into the swab was removed from the swab via pinching of the plastic tube as the swab is pulled out. Unlike previous iterations of the tests, the swab could be removed immediately after soaking and mixing of the fluids. The buffer vial had an attached lid with a nozzle. The lid was attached after the swab was removed and 3 drops were squeezed onto the sample plate. 10 minutes after the initial drops were applied, the sample result was observed. One red line next to the “C” symbol indicated that the test was functionally normally. One red line next to the “T” symbol indicated that the result was positive. No other anomalies indicated that the sample results were reasonably reliable. Detailed instructions can be found at btnx.com/covid19athome.

    The tests were taken beginning on Oct 3, 2022 back when the test subject woke up with a fever. 2 samples were taken during the first 36 hours (midday 1, evening day 2). Both tests resulted in “negative” scores on the rapid tests. These tests are not included in the visual analysis of the COVID positivity progression and were used to calibrate expectations. The third test was taken in the evening of day 3 and resulted in a faintly positive score. Subsequent tests were taken in the evening each day. The tests were aligned each night and it was observed that while the fabric/wicking material of the samples were drying out, the intensity of the red lines remained similar to their initial conditions at the end of the 10 minute waiting period. Images of the collected tests were taken using a OnePlus8T+5G phone using the default camera settings. The lighting available for the image was a 3 panel white LED approximately 20 cm above the middle of the samples. The photos were taken after nightfall and with no other illumination sources.

    The selected “best” image was cropped to only include the samples to reduce any external interference (Fig.2). As the image was taken with a relatively perpendicular shot, additional skew was not required for the image. Boxes where the reference line (C-line) and the test line (T-line) were selected. The RGB pixel values were extracted from the the boxes for the 10 samples that were aligned next to each other. The values from the C-line and the T-line were then compared to each other in a few different ways to demonstrate the progression of having COVID to testing negative.

    Figure 2. Cropped image containing results of the COVID19 Rapid Tests as taken by a cellphone camera. The last two tests are negative (no visible reading in the T-line).

    Results: The RGB values were selected in pixels in xy dimensions of x by y pixels. This resulted in 100 pixels in each box selection. Isolating only the R-value for the C-lines (which one would potentially expect to be the most useful) provided a clear pattern where the R value is lowest when the pixel includes the C-line. In retrospect, this should be fairly straightforward to understand as the “white” background pixel is created from high values of all RGB components (256).

    A plot of the maximum RBG values is shown for each one of the C- and T-lines in Figure 3. A clear maximum value for the T-line can be seen from each RGB component from samples 5 and 6 with a steep fall-off towards a minimum value with sample 8. Figure 4 shows the “normalized” R values for the T-line based on the minimum R-value in each sample test and scaled by the minimum R-value from the C-line.

    Figure 3. Minimum RGB values in the area for the C-line (circles) and T-line (triangles). The difference in value can potentially be attributed to unbalanced lighting.
    Figure 4. Normalized R-values for each sample (minimum R in T-line divided by minimum R in C-line).

    Discussion: Visual inspection of the COVID19 Rapid Tests would suggest that there was a rapid increase in the “redness” of the T-line in the first 3 days, with a slow taper off. It is possible that the saturation of the red is actually quite similar from test to test, and it is the thickness of the T-line that varies. In such case, checking the contribution to the R-value is not a useful indicator of “positiviness”. Instead, the thickness of the lines should be considered. In addition, there were no redundant samples. Future studies should consider 3 rounds of swabbing and taking the average metric of each sample run.

    Conclusions: A faint positive is still positive. COVID sucked, but I was fortunate enough to not lose my sense of smell for too long (likely a blocked nose). We shall see about long-COVID.

    References: Me.

    Editor 2: …

    Supplementary Material: Images from homemade meals during this time are included in this section. Image S1 includes a noodle soup with noodles made from scratch (I think). Image S2 is a mysterious fried rice concoction.

    S1. Noodles. Yum.
    S2. Fried rice!
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  • Hello World!

    This is Elisa. Abstract-ED is the blog. More to come.