James Kane

@jameskane.blog

356 Followers 362 Following

Software Engineer. Retro Computing. Genetic Genealogist. Fitness Enthusiast. TTRPG Gamer. Living the in the American Midwest.

A screenshot of the Decoding Us Y-DNA tree with a detailed information panel open on the right. The tree shows various branching haplogroups, and the side panel displays specific genetic data for the selected node "R-S1115," including its TMRCA (Time to Most Recent Common Ancestor), specific SNP mutations, and Y-STR ancestral motifs.
A phylogenetic tree diagram of Y-DNA lineages from the Decoding Us project. The chart shows a branching ancestral path starting from a root "Y" node, splitting into major branches like A0-T and A1, which further divide into numerous smaller sub-clades (yellow boxes) with associated variant counts and TMRCA (Time to Most Recent Common Ancestor) dates.
A Linux terminal window showing system information fetched via a neofetch-style tool. On the left is the Ubuntu logo in red ASCII art. On the right, the system specs read: jkane@CIX-Phecda-Board; OS: Ubuntu 26.04 LTS (Resolute R4); Host: CIX Phecda Board (1.0); Kernel: Linux 7.0.0-38-cix; Uptime: 3 mins; Shell: bash 5.3.9; DE: GNOME 50.1; WM: Mutter (Wayland); CPU: Cortex-A720*2 + Cortex-A520z; GPU: Mali-G720 MC10 [Integrated]; Memory: 5.54 GiB / 29.82 GiB. A row of color palette blocks sits at the bottom of the text.
A web browser screenshot of the Decoding Us platform developer region displaying an interactive mitochondrial DNA (mtDNA) phylogenetic tree layout. The interface shows a horizontal tree structure focusing on haplogroup U5a1 and its nested subclades, including U5a1b1, U5a1b1a, and U5a1b1h. Internal nodes are represented by light yellow rectangular boxes labeled with haplogroups or specific variants (such as '★ chrM:15743C>T'). Terminal nodes branch out to individual sample identifiers from the 1000 Genomes project, marked by green dots (e.g., NA20515, HG00285). The top of the page includes a breadcrumb navigation path tracing the phylogenetic lineage back to root nodes, alongside controls for tree depth and orientation.
A screenshot of the "About This Mac" window. It shows a Mac Pro (Late 2013) running macOS Monterey version 12.7.6. Specifications listed include: Processor 2.7 GHz 12-Core Intel Xeon E5, Memory 64 GB 1866 MHz DDR3, and Graphics AMD FirePro D700 6 GB. The serial number is redacted with a black bar.
A dark-mode application screenshot of "DUNavigator" showing the "Data Sources" tab for subject KANE-001. Sequencing Runs: Lists multiple genomic sequencing datasets including: Whole Genome Sequencing via Illumina NovaSeq (615.6M reads, paired-end, sourced from YSEQ). PacBio HiFi WGS via PacBio Sequel II (1.1M reads, single-end, sourced from Dante), which features a nested alignment bar for chm13v2.0 pbmm2 with 3.6x coverage. A second Illumina NovaSeq WGS run (651.8M reads, paired-end, sourced from Dante). Full Genomes Y Elite via Illumina iSeq (62.1M reads, paired-end, sourced from FGC). Chip / Array Profiles: Displays three collapsed accordion menus for array data: 23andMe (1,407,553 markers, 96.8% call rate), AncestryDNA (701,474 markers, 97.9% call rate), and BiSDNA chromo2 (14,219 markers, 99.9% call rate). STR Profiles: Displays collapsed menus for short tandem repeat data, listing a Y-111 profile with 102 markers from FTDNA and a Y-12 profile with 16 markers from YSEQ.
A dark-mode application screenshot of "DUNavigator" showing the "mtDNA" analysis tab for subject KANE-001. mtDNA haplogroup panel: Displays the assigned haplogroup as U5a1b1g, noting "53/55 mutations, score 0.629". It maps out the full phylogenetic lineage tracing back to RSRS. mtDNA sequences panel: Indicates "No mtDNA sequences yet" with a button to "Import mtDNA FASTA". mtDNA de-novo SNP calls (chrM) panel: Displays a list of "28 SNP call(s)" with columns for Position, Change, Depth, and AF (Allele Frequency). Visible variants include transitions like 174 A>G (depth 52, AF 1.00), 2620 T>C (depth 83, AF 1.00), and 6451 C>T (depth 109, AF 0.99). A disabled "Publish variants to PDS" button is visible at the bottom of the list.
A dark-mode application screenshot of "DUNavigator" showing the "Y-DNA" analysis tab for subject KANE-001. Y haplogroup panel: Displays the assigned haplogroup as R1b1a1b1a1a2c1a3a2a1a2d1b1, supported by 6 runs with a confidence score of 0.52. A "Callable mask" is checked and noted as "self-referential (this sample)". Y variant profile section: Displays a terminal classification of R1b1a1b1a1a2c1a3a2a1a2d1b1 (2 confirmed, 0 novel, 0 conflict, 0 single-source, confidence 1%). A table below lists specific SNPs (such as L419, M91, and various AS/A series markers) along with their position, ancestral/no-call state, confirmation status, and data sources (WGS or chip). Private Y (donor union) panel: Displays "400 novel + 33 off-path" variants relative to the terminal R-FGC29071. The accompanying table lists genomic positions, nucleotide changes (e.g., A>G, T>C), sequencing depths (ranging from 8 to 28), and classification categories like "novel" or "off-path" with specific haplogroup branches.
A dark-mode desktop interface of "DUNavigator" showing the "Overview" tab for a male subject, KANE-001. The top section, "Haplogroup consensus", displays: Y-DNA: R1b1a1b1a1a2c1a3a2a1a2d1b1 (6 sources, conf 0.519) marked as compatible. mtDNA: U5a1b1g (6 sources, conf 0.630) marked as compatible. The middle section, "Coverage", shows global metrics such as a Genome Territory of 3117292070, Mean Coverage of 3.63, Median Coverage of 3, and 1.1% of bases at or above 10x depth. A "Per-contig coverage" table breaks down stats for chromosomes 1 through 6 (chr1–chr6), showing lengths, read counts, and mean depths ranging from 3.71 to 4.10. A "Depth histogram — whole genome" with red vertical bars is visible at the very bottom.
A dark-themed desktop software interface for "DUNavigator: Decoding-Us Navigator". On the left sidebar, a subject named "KANE-001" is selected, displaying a Y-DNA haplogroup beginning with R1b and an mtDNA haplogroup of U5a1b1g. The main panel displays the "Ancestry" tab for this subject. A section titled "Donor ancestry (best source)" shows a blue circular graphic and states "European 100.0%" with "19023/20000 SNPs - confidence 96%". Below this, a sub-breakdown lists specific European regions: NW European (Utah) 36.8%, British 23.6%, Tuscan (Italy) 14.2%, Iberian (Spain) 13.1%, and Finnish 12.0%. The bottom features a PCA (Principal Component Analysis) scatter plot comparing the sample against reference populations, and an error status bar at the very bottom of the window indicating a failed file fetch from a UCSC database URL.
SpaceMit AIBox-K3 Geekbench 6 Scores: 327 Single-Core, 1594 Multi-Core
Navigator's new Overview page showing a summary of data sources, and dashboard widgets for Y-DNA, mtDNA, Y-STR panels, and future Ancestry and IBD analysis tools.
New Navigator UI prototype featuring 4 different BAM/CRAM alignment files, two Chip results, and a running analysis progress bar. Each section has basic meta-data derived from the source files during the import process.
Preview of a Tree Diff in the in-progress development for Decoding Us.
A screen shot of the Decoding Us landing page featuring the first registered user logged in via their AT Protocol identity.
BAM Statistics report from decoding-us-tools's coverage module. Shows detection of the reference, sequencing platform, and read metrics. The dropdown provides an assessment of each contig's ability to be called.
New callable regions report generated from a short-read WGS BAM. Summarizing the Y chromosome alignment characteristics.
Heat map of global human biosamples in public repositories. Showing a clear preference in geographic sampling of Europe and the United States.
Limited Edition cover of Kobold Press’s Campaign Builder Dungeons & Ruins. Featuring gold and red foil dragon.
A SNP call chart showing Ancestral and Derived calls for members of a YDNA subclade.
hs1 aligned chrY callable coverage plot for HG00117.
STR Panel preview functionality showing flexible STR panel tables groupings my subclades.
Picture of the repaired 32” display panel with the MacOS Sequoia stock background image.
The STR Matches report showing the new button for your matches who allow contact for genealogical purposes.
A view of the sample provider's new Studies page. Shows enrolled studies with buttons to view, manage shared MDPA information shown in the project and to remove themselves. There's a second list of studies that the sample provider would fit based on the recruitment rules of the Study. There's an ability to Join or View the Study for more details.
New menu of public facing Y DNA Studies with brief synopsis of the projects and the investigators.
Early UI design layout of User preferences allowing them to enable Two-Factor Authentication or remove Users from their block list.
Threaded message reader for communication with recent DNA matches or Study members. Showing ability to reply or remove the message, and block troublesome members.
Top artists from my Apple Music account on 2024: Billy Squire, Genesis, Fleetwood Mac, Pink Floyd, Sammy Hagar, Queen, The Police, REO Speedwagon, Boston, and ELO.
System activity on a 24-core system showing high utilization.
Image of dead black bands of pixels on a 32" monitor.
1980s Commodore 64 advertisment comparing IBM PC jr.
Cyberpunk 2077 coming to macOS on Apple silicon in early 2025.
Screenshot of AI slop explaining a graph of heart rate data in Strava’s iOS application.
Tales of the Valiant Game Master's Guide
Everyday Heroes Core Rulebook & Highlander accessory