Recent content on Bjonnh.net
Over the past two decades, quantitative structure–activity relationship (QSAR) modeling has evolved substantially, driven by improved data accessibility, open-source descriptor generation, mature machine learning libraries, and scalable cloud computing. Large-scale benchmarking studies using public datasets have demonstrated the feasibility of building predictive models across hundreds of…
I made a tiny device that uses pressure from my mouth to control MIDI.
A simple right-click menu option to launch containerized Jupyter notebooks in any directory.
Natural products (NPs) continue to inform the discovery and development of a diversity of drugs, both marketed and investigational. Pain, one of the most common of human experiences and profound challenges in medicine and biology, has emerged at the core of an urgent societal problem, in the United States and globally. The present study employs a retrospective analysis of an extensive set of…
This exploratory study was designed to identify factors implicating microbial influence on medicinal plant metabolomes. Utilizing a whole-microbiome approach, amplicon sequencing was used to identify the makeup of fungal and bacterial assemblages from endophytic (interior) and epiphytic (external) environments in two different sets of congeneric host-plant pairs, with collection of multiple…
I’m organizing a MIDI workshop at PumpingStation One sometime in 2024. I decided to try to Work with the garage door up , and share everything as I am doing it. This is not meant to be a full-fleshed finished documentation more splattering my brain on a wall so I can see more clearly
DINOctopus is a 10 ports small device made that can merge/split/mix MIDI signals and act as a USB interface.
A small (28x21mm) MIDI board for your microcontroller projects. Especially for RP2040/Pico projects or other 3V3 boards.
A class on Open Source based FPGA programming at the local hackerspace.
Phytochemical investigation of Marsypopetalum modestum (Annonaceae) led to the isolation of a new phenylpropanoid glycoside, lyciumphenylpropanoid B (10), along with nine known compounds (1-9) from an aqueous methanolic extract of the stem. Most compounds are reported from this genus for the first time. The structures of the isolated compounds were elucidated using spectroscopic methods including…
The Akai MPC One is a nice device, but it is a pain to backup if you have to get the SDCard out everytime.
Using the SSH mod discovered by TheKikGen , it is easy to connect over
ssh and get whatever you need.
Lotus search 
 Lotus search is a tool to search for compounds and taxa in the Lotus database. 
 
 What is LOTUS? 
 The LOTUS database is a database of natural products, their associated producing organisms and
the bibliographical references in which the discovery or identification was made.
It is hosted on Wikidata as the main source of truth. 
 It is the result of a…
An evaluation of select medicinal species from Chapter 5 was performed by exploring the global scientific literature for evidence in support of the folkloric uses, through convergence in bioactivity profiles or corroboration of therapeutic uses. Five common affliction categories in the primary ethnopharmacological data were explored: diarrhea, fever, pain, rheumatism, and liver complaints. The…
On using 3d printer screens and controllers for your own projects. 
 I bought some of those cheap 3d printer controllers on the big evil site for $12: BigTreeTech Mini 12864.
There are other similar ones in the same price range from other brands, but I can’t guarantee they have the same pinouts and controllers. Also these came with a tiny yellow rubber duck, always useful when you…
FauxDIS is an educational resource loosely inspired from the FBI’s CODIS database.
I recently got a WD SN850. There is a little trick to do when you receive it to switch it to 4k LBA and thus getting better performance by using native block size.
Contemporary bioinformatic and chemoinformatic capabilities hold promise to reshape knowledge management, analysis and interpretation of data in natural products research. Currently, reliance on a disparate set of non-standardized, insular, and specialized databases presents a series of challenges to data access, either within the discipline or to integration and interoperability between related…
Two new diprenylated coumaric acid isomers (1a and 1b) and two known congeners, capillartemisin A (2) and B (3), were isolated from Artemisia scoparia as bioactive markers using bioactivity-guided HPLC fractionation. Their structures were determined by spectroscopic means, including 1D and 2D NMR methods and LC-MS, with their purity assessed by 1D 1H pure shift qNMR spectroscopic analysis. The…
Curcuma longa (turmeric) has an extensive history of ethnomedical use for common ailments, and “curcumin”-containing dietary supplements (CDS) are a highly visible portion of today’s self-medication market. Owing to raw material cost pressure, CDS products are affected by economically motivated, nefarious adulteration with synthetic curcumin (“syncumin”), possibly leading to unexpected…
I finally put my hands on a Trinket M0 for the Trackpoint . Meaning, no more ugly driver.
A friend of mine Pierre Grangé-Praderas needed to make a webpage with graphs. So I decided to play with Cytoscape and Hugo and see if I could integrate them together.
I spent a day adding a trackPoint to my keyboard to avoid having to move all the
time to the trackball. I wanted something that would allow me to quickly jump from one window to another while keeping my hands on the keyboard.
This Perspective of the published essential medicinal chemistry of cannabidiol (CBD) provides evidence that the popularization of CBD-fortified or CBD-labeled health products and CBD-associated health claims lacks a rigorous scientific foundation. CBD’s reputation as a cure-all puts it in the same class as other “natural” panaceas, where valid ethnobotanicals are reduced to single, purportedly…
In a continuing search for neuroprotective stilbenoids, two uncommon
diastereomeric stilbenoid glucosides, africanoside A (1) and B (2) as well as
fifteen known stilbenes, E-resveratrol, E-gnetifolin E, E-piceid,
E-resveratroloside, E-gnetifolin K, E-gnetol, E-isorhapontigenin,
E-isorhapontin, E-isorhapontigenin-4′-O-glucopyranoside, E-gnetin C,
E-bisisorhapontigenin B,…
Chlorophylls are present in all extracts from the aerial parts of green plant materials. Chlorophylls may act as in vitro bioassay nuisance compounds, possibly preventing the reproducibility and accurate measurement of readouts due to their UV/vis absorbance, fluorescence properties, and tendency to precipitate in aqueous media. Despite the diversity of methods used traditionally to remove…
During my PhD, I was working with devices that help separating components of mixtures and devices to analyze these components. However, a lot of manual handling of samples was required between these different devices. So I decided to re-purpose an existing device to solve that. After a little bit of reverse-engineering and the development of a custom control software, problem was solved.
Finally, I am trying to reorganize this website, add a portfolio and other kind of stuff that will help me remember the ton of stuff I wrote but never talked about. I’ll document in this article the different kind of things I tried. I am especially excited by the portfolio aspect (of which most will be private though).
CENAPT Navigator is a compilation of resources related to Natural Product Research and Pharmacognosy. It includes resources on molecular structures, biological activities, spectroscopic data, bibliography, genetics, diseases, pathways, metabolomics…
NAPRALERT is a leading database containing >40 years of the natural products literature.
This website has been made with Hugo and a custom theme that involves a lot of css, html, templates.
Whereas generic, LC-based pharmaceutical control quality procedures depend largely on the detection mode and can be particularly ‘blind’ to certain impurities, NMR is a more versatile and, thus, often more judicious detector. While adulteration presents ever-evolving challenges for the analysis of active pharmaceutical ingredients (APIs) and finished products sold in the worldwide (online)…
Mass spectrometry (MS) offers unrivalled sensitivity for the metabolite profiling of complex biological matrices encountered in natural products (NP) research. The massive and complex sets of spectral data generated by such platforms require computational approaches for their interpretation. Within such approaches, computational metabolite annotation automatically links spectral data to candidate…
Took me some time to learn how SNMP v3 (and SNMP in general) works. But now I have nice dashboards.
Ensuring identity, purity, and reproducibility are equally essential during synthetic chemistry, drug discovery, and for pharmaceutical product safety. Many peptidic APIs are large molecules that require considerable effort for integrity assurance. This study builds on quantum mechanical 1H iterative Full Spin Analysis (HiFSA) to establish NMR peptide sequencing methodology that overcomes the…
When using docker in LXD/LXC, the FS performance is really really bad.
I needed to run Docker in LXC containers on my Ubuntu servers.
I’m now a heavy user of Draw.io a great piece of Free software from jgraph . However sometimes I need to use it offline… Here is an easy guide on how to use it locally.
I’m moving all my old file-based ssh and gpg keys to a YubiKey 4 hardware key. This post will get updated with a few notes along that migration. It also covers how to use pass and pass-tomb with these. And then I fell down the rabbit hole of using those keys everywhere…
With contributions from the global natural product (NP) research community, and continuing the Raw Data Initiative, this review collects a comprehensive demonstration of the immense scientific value of disseminating raw nuclear magnetic resonance (NMR) data, independently of, and in parallel with, classical publishing outlets. A comprehensive compilation of historic to present-day cases as well as…
[Draft published as is, this is old.] I am playing with Pulsar and Heron in Kotlin. And I was always struggling with getting my kotlin project packaged properly. Here is a walk-through.
I was complaining on IRC about someone sending me a screenshot as a word file. Then my friend Aaron Lav had a comment that I turned into that project.

 Humans have co-evolved alongside numerous other organisms, some having a profound effect on health and nutrition. As the earliest pharmaceutical subject, pharmacognosy has evolved into a meta-discipline devoted to natural biomedical agents and their functional properties. While the acquisition of expanding data volumes is ongoing, contextualization is lagging. Thus, we assert that the…
How to update the PERC6/i firmware from Linux.
We had this conference in Chicago
in 2016. As I was playing with the laser-cutter and making planetary motion
devices see Here , I also was playing with the idea of circular slide rulers. 
 As the calculation of elution volumes and retention in CCC and CPC are using
multiplications and divisions it is possible to do these on a circular slide
ruler (or a normal one) by using…

 
 
 
 
 
We had [this conference](https://gfp.people.uic.edu/ccc2016/) in Chicago
in 2016. As I was playing with the laser-cutter and making planetary motion
devices, Guido asked if it wouldn't be possible to make two awards for the
conference. I also made a [Slide ruler](/article/20170530_cccslider) for that conference.
 
 A bit of design,…
This is an answer to some reactions to our review article on Curcumin.