I will just leave these quotes here …
Veerabhadran Ramanathan, a professor at the Scripps Institution of Oceanography at University of California, San Diego, explained that many polluting particles have a “masking” effect on global warming, reflecting the sun’s rays, canceling out some of the warming from greenhouse gas emissions. With that shield of pollution gone, Ramanathan said, “We could see an increase in warming.” — Grist, Shannon Osaka
Militant nurses, antibiotic-resistant super-bugs
Militant nurses, our national social conscience, are making sure that we all understand the grave dangers created by inadequate stockpiles of protective supplies like N95 face masks. They also remind us that hospitals have become greenhouses for antibiotic-resistant super-bugs such as C. difficile, which may become major secondary killers in overcrowded hospital wards. …
Troubled times. But we live, we breathe, we write.
Recently I translated a poem from Dutch into Bangla.
The poem — “Vogels, vissen” — is by Ingmar Heytze. He is a prominent Dutch poet and writer who was the first to be officiated as the Utrecht city poet in 2009. A link to the original Dutch text and the poet’s reading.
Below is my translation. Thanks to Alam Khorshed (Founding Director of Bistaar) for his generous help in editing and improving the quality of the translation.
বঙ্গানুবাদ: শরিফ ইসলাম
সম্পাদনা: আলম খোরশেদ
রেডিওটা বন্ধ করো। যা শোনার সবই শুনেছ। নিস্তব্ধতাই সবচেয়ে সহিষ্ণু।
পত্রিকাটা ভাঁজ করে পাশে রেখে দাও। আসার আগেই ওটা পুরনো হয়ে গেছে।
সার্চ, শেয়ার আর লাইকের নামে বুড়ো আঙুল দেখাতে দেখাতে তুমি নিজেই যেন
চোখে সর্ষে ফুল দেখতে শুরু কোরো না।
শেষমেশ পর্দাটাকে একেবারে কালো করে…
In this post, I describe how to use Python to compare two DNA sequences from two different databases. This is not about any specific scientific use case. I am primarily interested in the details of different APIs and data structures that deal with sequences. I am also interested in data interoperability and FAIR. This example will break down things with a very specific string comparison exercise which can be a small building block for a complex distributed data infrastructure.
One of the common ways to represent Nucleobases like DNA is simply with a succession of letters like ‘TACGCTGTTATCCCTAAAG’. So, in essence, all we are talking about here is comparing two sets of strings. Of course, there are other methods to verify sequence fingerprints and data traceability but here I am just focusing on the sequence alphabets (a use case here is to perform sequence similarity searches that identify which sequence entries are identical or similar to each other). …
In this post, I want to continue the thought process regarding event-driven architecture (see my previous post on event-driven digital object architecture). This time add Blockchain to the mix.
Below is an example using easychain (a set of python scripts) that does a brilliant job in explaining the fundamental concepts of a blockchain. I am not implementing any particular Blockchain technology, also not exploring all the aspects (such as distributed consensus and mining), just the idea of hashed ledger to show the possibility of a decentralized, tamper-proof, transparent system.
In this example, I make use of the natural history museum data landscape where the physical specimens are the source of primary data for various research questions. A similar infrastructure could be implemented without Blockchain, but one question that is worth exploring: what value would a Blockchain implementation provide? …
It was a light gray 1990 Ford Taurus, and I took possession of it in 2003. At that point, the Taurus was already in its advanced age (110,000 miles!). I responded to a Usenet classified ad posted by a Chinese graduate student who was going back to his country after graduation. I just got my first real job at that time. When I saw the $500 offer, I decided to go for it.
Well, it was a piece of junk. But I loved it, used it, and abused it for almost three years. It had a tape deck so I could use all of my old mixed tapes there. It was perfect for running errands around town but not capable of long hauls. I didn’t mind. It also worked as a community service vehicle. …
In this post, I want to share some of my initial thoughts about building a service with the event-driven and event first approach. Below I use examples that are related to the biodiversity, natural history collection, and the museum world. I also use the concept of Digital Specimen — a specific form of the more general-purpose Digital Object (DO), which is defined by Digital Object Architecture (DOA). My goal is to see how we can fuse the event-driven model with the object-oriented aspect of Digital Object. Using specific domain-related facts (i.e., the fragmented data landscape), we can create semantics and properties and store them as events so any process and service can be mapped. …
Excited about these two recent acquisitions.
The fact is that not sure how much I will be able to tackle Lucy Ellmann’s Ducks, Newburyport but I could not resist. I first saw and learned about her and this book when I was visiting Dublin a few months back. And last few weeks it has been prominently displayed at my local bookstore (Mayflower Bookshop Leiden, The Netherlands). And Nate Chinnen’s book was discovered at the cool Mondriaan Jazz Festival last week.
I also recently started using git to track my finished reading list. Check it out!
Recently I have been exploring different kinds of R packages that deal with biodiversity and ecology data. This is partly to understand the fragmented and distributed data landscape that we are tackling in DiSSCo. Our goal is to build a new world-class Research Infrastructure (RI) for natural science collections. Also, an excuse to learn something new and share with the wider community.
I discovered that R is immensely popular in biodiversity and ecology research. There is an active community that maintains various packages that are well-curated with easy to follow examples. Of course, all of these can be done with Python or any other languages — often it boils down to the task at hand. However, the design of R is closely aligned with statistical methods and data exploration which makes it handy for large datasets like species occurrence data. For example, a package called BioFTF provides a functional analysis tool that helps understand the multivariate approach of biodiversity (not just species abundance and richness). This a very domain-specific package that takes advantage of R’s statistical features. …
In this post I want to talk about how user stories can help us during the conceptual design of a large, distributed data infrastructure. Before thinking about connecting, aggregating and linking various data sources, I find it useful to focus on a particular scenario and think about the related data components.
Currently, I am involved (as the Data Architect) in the DiSSCo (Distributed System of Scientific Collections) project where with the help of the wider research and data community we are trying to understand the natural science collections data landscape. Alex Hardisty described this process as “fishing in deep pools for something you know is there but can’t see”. Even though our user stories are collected from the natural history museum and biodiversity community, I hope this is also useful for a general audience. I will keep some of the gory technical details (such as RDF, Darwin Core) out of the way to illustrate the basic problem. …
I guess I can call this my “mid life” crisis. At least not as expensive as buying a red sports car. At least one of them is red….
I currently own three different notebooks for three different purposes and I am learning to write again with a fountain pen, draw figures and cartoon faces and trying to take notes using Sketchnotes technique (there are gazillion entries on it in the interwebs so not linking anything here, go look up if you want to know more about skechnotes and bullet journaling). Yes, I sometime doodle at work. …