BIOLOGY & SCIENCE
Navigating the Global Bioinformatics Database Ecosystem: A Practical Taxonomy
From primary archival repositories (NCBI, EBI, DDBJ) to curated structural and pathway atlases: where modern biological data lives and how it connects.
WRITING
All Articles
Essays, notes, tutorials, and other things I've written about biology, science, technology, and life.
“Sometimes a simple observation can open a larger question.”
BIOLOGY & SCIENCE
Understanding Gene Expression: From a Beginner’s Perspective
A gentle introduction to how cells turn genetic information into function.
TUTORIALS
Working with Genomic Data in Python (Beginner-Friendly)
A practical introduction to handling FASTA, sequence analysis, and basic visualization using Biopython.
REFLECTIONS
On Curiosity and the Long Road
A personal reflection on navigating computational biology from Indonesia, the power of open data, and why honest curiosity endures.
REFLECTIONS
The Beauty of Small Systems
Why minimalist architecture and modular design triumph over monolithic complexity in biology and code.
CREATIVE WRITING
The Last Greenhouse: Notes from the Field
Observations on wild medicinal germplasm, classical botany, and the race to digitize living archives before they disappear.
BIOLOGY & SCIENCE
The Value of Slowness in Science
In a world obsessed with velocity and metrics, slowing down is the ultimate form of intellectual precision.
SCIENCE COMMUNICATION
Why Biology Needs Better Computational Thinking
Moving beyond wet-lab intuition: why biological research now requires algorithmic precision and data hygiene.
TUTORIALS
Introduction to Bioinformatics Workflows: From Raw Reads to Biological Insight
A practitioner's architectural blueprint for structuring scalable, reproducible NGS pipelines with Nextflow and Snakemake.
BIOLOGY & SCIENCE
Why Conserved Genomic Regions Matter
Exploring nucleotide invariance across evolutionary epochs and what purifying selection reveals about biological necessity.
TUTORIALS
Getting Started with Primer3 (for Genomic Analysis)
A practical, test-driven guide to automating PCR and qPCR primer design using Python and thermodynamic modeling.
TUTORIALS
Understanding RNA-Seq Normalization: TPM, FPKM, and Beyond
Resolving sequencing depth, gene length dependencies, and library composition biases in differential transcriptomics.
BIOLOGY & SCIENCE
When Microbes Meet Cancer Biology
Intratumoral microbiota and metabolic rewiring in solid tumors: pathogen, bystander, or therapeutic lever?
REFLECTIONS
On Not Knowing: Cultivating Intellectual Humility in Science
Why the most productive sentence in computational biology is 'I do not know, let us write a simulation and test it'.
TUTORIALS
From FastQ to Matrix: Quality Control at Scale
Detecting adapter contamination, GC-skew anomalies, and optical duplicates before alignment: defensive workflows for high-throughput sequencing.
BIOLOGY & SCIENCE
The Architecture of Mitragyna Speciosa Alkaloids
Dissecting the biosynthetic pathway, indole-secoiridoid scaffolds, and atypical opioid receptor pharmacology of Kratom secondary metabolites.
REFLECTIONS
Reproducibility is a Habit, Not a Checkbox
From pinning conda environments and deterministic seeds to automated pipelines: building scientific workflows that survive time.
SCIENCE COMMUNICATION
Why Communicating Science Clearly Matters
Breaking down complex genomic architectures without diluting academic truth: a manifesto for clear writing.
BIOLOGY & SCIENCE
Chromatin Remodeling and Epigenetic Memory
How histone acetyltransferases, SWI/SNF complexes, and DNA methylation preserve cellular identity through mitotic cell divisions.
TUTORIALS
Writing Fast Code for Heavy Biological Strings
Benchmarking Python, vectorized NumPy, Cython, and memory-mapped files for high-throughput genomic string operations.
BIOLOGY & SCIENCE
The Logic of Biological Networks
Scale-free topology, feed-forward loops, and why molecular circuits exhibit robust resistance to random component failure.
TUTORIALS
Phylogenetics Without Tears: Alignment to Trees
Maximum likelihood substitution models, bootstrap convergence, and tree visualization with modern computational pipelines.
BIOLOGY & SCIENCE
Comparative Genomics of Cold-Adapted Microbes
Membrane fluidity, proline substitutions, and thermal stability in psychrophilic bacteria surviving subzero polar permafrost.
REFLECTIONS
The Unfinished Manuscript on My Desk
Facing dead ends, negative results, and the quiet courage required to set aside flawed hypotheses.
BIOLOGY & SCIENCE
Epigenetic Regulation of Plant Flowering
Vernalization, histone methylation switches at the FLOWERING LOCUS C, and environmental sensing in Arabidopsis thaliana.
BIOLOGY & SCIENCE
Synteny and Chromosomal Inversions Across Primates
Collinear gene blocks, breakpoint fragility, and the genomic rearrangements that shaped human and primate evolutionary history.
TUTORIALS
Automating Biological Sequence Tasks with Python
From tedious web form submission to programmatic pipelines: batch fetching, FASTA sanitization, and automated translation.
BIOLOGY & SCIENCE
CRISPR-Cas9 Mechanics: Beyond the Molecular Scissors Metaphor
Deconstructing guide RNA thermodynamics, PAM constraints, and computational off-target prediction in precision genome editing.
BIOLOGY & SCIENCE
The Basics of Genetic Engineering: What Textbooks Don't Tell You
From restriction digests and ligation failures to synthetic biology circuits: the practical realities of manipulating recombinant DNA.
BIOLOGY & SCIENCE
Digital Biology and the Modern Genomic Landscape
From static genetic codes to dynamic cellular computation: how high-throughput genomics and bioinformatics transformed biological science.
CREATIVE WRITING
Letters from the Field: Rain, Mud, and Broken Pipettes
Dispatches from botanical sampling expeditions in the tropical rainforests of West Java.
CREATIVE WRITING
The Quiet Chemistry of Lichen
Symbiosis, depside metabolites, and the slow weathering of alpine stone over centuries.
CREATIVE WRITING
Echoes in the Forest Canopy: Acoustic Ecology of Tropical Birds
Listening to the soundscapes of Halimun Salak: bioacoustics, territorial choruses, and passive sensor arrays.