Hey Rohit, what’s happening NOW?
So a website with a link that says “now” goes to a page that tells you what this person is focused on at this point in their life. For short, we call it a “now page”.
Note: Periodic updates from this NOW page can also be retrieved by finger rohit@rohitfarmer.com
Location
North Bethesda, Maryland, USA
Non-tech/personal
On going thoughts & status
These statuses are toots from my Mastodon profile at https://mindly.social/@ro
Periodic updates
June 3, 2024
It was a sad and frustrating start to May. I had three of my fishing rods stolen from the garage of my apartment building. I returned from camping, and while unloading the gear from the vehicle, I left the rods leaning against the wall in the garage, thinking that I would take them up on the next trip. But I forgot and left them overnight before realizing that they were not at home. The next day, I checked all the lost and found places in my apartment building but couldn’t find them. Losing the rods was not as disturbing as the leasing office’s response to helping me find them. I wrote a blog post about it with the details here.
We celebrated Eva’s 3rd birthday in the club room of our apartment building. On the same day, one of Eva’s daycare buddies also had her birthday, so Eva and I attended her friend’s birthday party in the morning and celebrated her in the evening. For Eva’s party, Sibyl cooked a lot of delicious food single-handedly.
Our neighbors Harish and family introduced us to Ice skating at the Wheaton Ice Arena. It was the first time we all did ice skating. I knew how to roller skate, so it was easier for me to pick it up. However, I did fall twice, trying to replicate my roller skating moves on the ice only to realize that the ice rink was as hard as a concrete floor. Sibyl, Elsa, and Eva used a supporter. While Sibyl and Eva only lasted 15 mins. Elsa continued skating with me for around 40 minutes. We all loved the experience and would add to our ever-growing activities list. Upon our return from the ice rink, we spotted a double rainbow. It was the first time Elsa and Eva saw a rainbow. All the colors were vibrant and so clearly visible.
I have started birding as a new hobby. Again, Harish introduced me to the Merlin Bird ID app, which detects bird species based on their sound. I don’t have any experience birding, but it seems Maryland is blessed with quite a few varieties of birds, both native and migratory. I wrote a blog post about my experience so far here. I clubbed the Merlin app with my long-forgotten binoculars and gave it a renewed purpose. It was only last week I detected a Northern Cardinal on the app and then spotted it hopping on the trees with my binoculars. Watching wildlife in their natural habitat gives a very different perspective and appreciation.
The weekend before last, we formally started our summer with a day trip to Sandy Point State Park’s beach. I rented a minivan and drove us and Harish’s family to the beach. This year, again, I set up my iconic one-of-a-kind beach shelter. Sandy Point Beach is on the Chesapeake Bay, so usually, the water temperature is warmer than the Atlantic Ocean. However, it does get jellyfish invasion during the mid and late-summer months.
On the same weekend, I also attended Birmingham University’s alumni meet in Washington, DC. It was the third year that I attended the meeting of our local chapter. I saw some repeat and new faces. Our oldest alumni was from the batch of 1981, and the youngest was from 2023.
This summer, I started playing the number plate game with my neighbors. We have to note down the names of all the states in the US from which we spot a car (number plate). The one who gets the most states spotted wins. That means we will have to be on the road as much as possible to increase our chances of spotting cars from many states. I have already spotted cars from 11 states so far.
Every year, I decide to improve and grow a couple of my hobbies. This year, I am fishing and birding, and the cool thing is that I can do both of them in the same spot. The usual places where I go fishing also have a decent variety of birds to spot. Hopefully, at the end of this year, I will write an annual report on how these hobbies progressed, what I was able to achieve, and some tips and tricks that I learned along the way.
Tech/professional
On going thoughts & status
These statuses are toots from my Mastodon profile at https://fosstodon.org/@swatantra
Periodic updates
May 1, 2024
In April, I mostly worked on metagenomics and PhIP-Seq data from two projects. I utilized CZID for metagenomics, which carried out host genome depletion and provided water contamination information in the form of z-scores per taxons that it had identified in the samples. Although CZID’s website is excellent, it was not clear that the water contamination depletion is not reflected in read counts but is presented in the form of z-scores, as mentioned above. We realized it when we saw the enrichment of taxons that did not make biological sense in the downstream analysis. Z-scores can only be exported sample-by-sample along with other information, such as taxonomic IDs. I had to write a function to combine these multiple sample-by-sample files into a combined file while filtering the taxons that did not meet our z-score cutoff. Filtering taxons using the z-scores has eliminated some of those problematic taxons that were seen as highly enriched.
For the PhIP seq analysis, we ran into an issue with another dataset that was generated using a smaller library/panel. Many of the tiles did not receive a p-value in the regression analysis, and it was not apparent why. My theory is that the phipstat code is performing several divisions, and in one of those divisions, the values are going smaller than what R can handle natively; hence, the values are rounded to zero, which is then passed to a log function, which returns an Inf value thus breaking the pipeline. I crudely fixed it to stop the optimizer in regression as soon as it hits an Inf value. This workaround does not break the pipeline, but for many tiles, the optimization terminates before convergence. A solution could be to allow R to handle long doubles using a package like Rmpfr. Another solution is to use larger tile libraries in our experiments. What is the sweet spot? I do not know.