si_pacbio
41J Blog
My contribution to the increasing entropy, and eventual heat death of the universe
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Recent Posts
- More Lasertec C130 Notes
- LaserTec C130 Notes
- Arducam Pivistation 5 Klarity I2C
- Pacific Biosciences Accuracy Notes
- Random Notes 5
- Unknown rotary valve (from Affy fluidics)
- BW Spectrometer Notes
- Random Notes 4
- PX-045A Printhead
- Random Notes 3
- Random Notes 2
- Epson UK Printheads (SX series)
- Random Notes
- E32-900T30D Module
- IRT-3000 IR Microscope Pics
- JFC-1100 Sputter Coater Pics
- VE7800 Filament Pics
- Pfeiffer TC600 Turbo Pump Driver Notes
- Keyence Ve7800 Notes
- Ve7800 Turbo Connection
- More VE7800 Pics
- Ve7800 Pics
- Some Awful Python Code
- Ion314 die images
- N choose K, with T targets. Probability of choosing at least one target
- Illumina iSeq (FireFly) IC Images
- Ubuntu 20.04 Fujitsu FAREHT1 Mouse/Touch Screen Fixes
- Siglent SSA3015X Plus Upgrade Issues
- Cost per Gigabase
- Global Sequencing Capability Notes
- Fujitsu FAREHT1 Laptop
- Playing with a Cepheid SmartCycler 2
- Startups and Japan
- DR4000U Repair and Filter Notes
- Newport 841-P-USB (Black case) Notes
- Inside the Lucira Check It COVID-19 Test
- Roswell Revisited
- Bio-rad SmartSpec Plus Spectrophotometer
- AxBio – Nanopore Sequencing Startup
- The Lunatic from Unchained Labs
- A quick look at some Theranos patents
- Mesoscale Diagnostics
- SomaLogic
- Quanterix
- Olink
- DU530 CFL Spectra – Again
- Nanodrop Notes
- Beckman DU530 Spectrophotometer CFL Spectra
- Beckman DU530 Photospectrometer (Hach DR4000?) Photodiode Amplifier Board
- Beckman DU530 Photospectrometer notes
- Nooma Bio
- Nautilus Prospectus Review
- QuantumSi Prospectus Review
- Nautilus Biotechnology
- Twinstrand Biosciences
- Dreampore – Protein Sizing
- Dreampore – Nanopore Protein Sequencing
- SBIR – America’s Training Program?
- Centrillion Update
- MiSeq Cost Analysis
- The Next Few Years in DNA Sequencing
- Singular Genomic Systems S-1 Review
- The Centrillion VirusHunter
- Armonica update
- DNA Sequencing and Japan
- Some Random Filters from eBay
- Genome Analyzer TIRF Alignment
- Photobeaching on the Genome Analyzer, using a IMX178
- Ultima Genomics
- Single Dye Experiments on a Genome Analyzer
- Z1 Coulter Particle Counter Teardown
- Genome Analyzer Quantum GEM 532nm Laser and filters
- Coulter counter/nanopore demonstrator
- LX-4000 stage controller notes
- Manteia Predictive Medicine
- GeneMind’s Single Molecule Sequencer
- The $15 Genome through reduced reagents
- QuantumSi’s Protein Sequencing Approach
- Lingvitae AS
- Are there mutations in SARS-CoV-2 CDC qPCR Primer Sites?
- Stratos’ Other Approach…
- Apton Biosystems Update
- Scripts to download SARS-CoV-2 replacements
- Singular Genomics Systems
- Single Technologies
- Element Biosciences
- Sony CCD-V8AF Video Camera Recorder – Viewfinder CRT Notes
- Sony CCD-V30 Camera Viewfinder CRT Notes
- Playing with a Handycam CCD-F340 Viewfinder CRT Notes
- Panasonic SJ-MR100 Notes
- Thoughts on a new approach to viral testing
- Issues Replicating Bioinformatics Papers
- Quick script to download Uniprot info for proteins from Pfam trees (Newick tree format)
- Kodak ES 4.0 teardown pics
- An attempt to read Pfam database dumps…
- ESC-30A Brushless DC motor driver Notes
- Sony CCD M8 Video Camera Notes
- Philips hair clipper PCB
- ILX511 CCD Interface r2
- DIL8 Boost converter design
- Notes on fixing a broken Gentoo grub install…
- ILX511 Interface PCB for ICE40HX8K
- ILX511 Update
- Notes on using a ILX511 Linear CCD, AD9225 ADC, ICE40HX8K and Nmigen
- Logomaker quick example
- ICE40HX8K AD9225 ADC with Nmigen
- Nmigen UART Notes
- Nmigen PLL ICE40HX8K/HX1K
- Various OP177 die images
- Notes on the Keithley 2002 ADC
- Multislope ADC Bring up (Dual slope)
- Thoughts on interviewing with YC as a science based startup
- Gene Editing Companies (December 2018)
- QuantumSi
- 2018 DNA Sequencing Raises and Acquisitions
- Thoughts on Ion Torrent and the iSeq
- How much does it cost to ship 1cm^2 of silicon?
- Stratos Genomics
- Illumina consumables are 90% profit?
- Evonetix and other thoughts
- An Encoding And Correction Approach for DNA Data Storage
- Using an SBS-like approach to selectively amplify
- Eve Biomedical
- Apton Biosystems
- Universal Sequencing Technology
- Read/Write DNA Devices – pt2
- Roswell Biotechnologies
- InSilixa
- iNanoBio
- QuantumDx
- DDC112 Board Design/Bring Up
- Reprogramming a ATTINY85 to use an external oscillator using the Arduino IDE
- DNA Synthesis Markets
- DNA Synthesis Research Groups
- Nanopore DNA Sequencing Research Groups (August 2018)
- Virtual Nanopores and DNA Synthesis
- Genapsys
- Sequencing with Mixtures of Three Bases
- Read/Write DNA Devices
- Iridia (was Dodo Omnidata)
- DNA Synthesis Companies (August 2018)
- Northshore Biosciences
- Direct Genomics
- Depixus (was Picoseq)
- Cygnus Biosciences
- Centrillion Technologies
- Caerus Molecular Diagnostics
- Bionano Genomics (Bionanomatrix)
- BGI – Miscellany
- BGI – Complete Genomics
- Minispin teardown pics
- Corning PC-420D Hotplate/Stirrer repair
- BGI Part 1 – Business
- Base4 Innovation Ltd
- Armonica Technologies LLC (now Inc)
- DNA Sequencing Companies (Updated May 2020)
- Inheco Control 96 + CPAC Ultraflat Notes (TEC/Peltier)
- 5517B Laser Tripod Mount
- Veeco/Bruker AFM (nanosope) head teardown pics
- uMD1 – ChipKIT 32 – HP Interferometer Interface
- uMD1 Build Notes
- Penrose Puzzle – Lessons Learned from Rev 0
- Dyeing 3D Printed Parts
- Embedding Electronics in Transparent Resin
- HP Interferometer Notes
- Genome Analyzer II Internal Pics
- Another iPhone MEMS Mic (different configuration+layers)
- The iPhone MEMS Mic in a SEM
- Throwing the BME280 Combined Pressure/Humidity Sensor in a SEM
- MXq – Quad Core Android Thoughts (and console kernel messages)
- 11inch Celestron CPC Series Telescope Repair – Initial Photos
- Moving a 1Kg Static Load
- The Hackerfarm Taobao Shuttle
- TSOP48 ZIF Socket Footprint
- A Note on Collaborations
- Fabricating oval through-hole pads
- A Brief Computational Analysis of “Pen-Pineapple Apple-pen”
- esp32 USB Stick (esp32 + ch340g + buck conv + sd card)
- Kicad esp32 schematic symbol
- The esp32 wroom32 design
- Dual esp8266 board
- Weird PCB Layouts with Kicad
- PIC Versus AVR
- Creating the miror swtich
- Random SEM Images – MCM68364 64KB ROM
- Ugly Solutions
- The AT24C01 and the AT24C01A
- The esp8266 and SD Cards
- The CL0116 Solar Lantern Controller IC
- FG-100 Soldering Iron Tip Temperature Sensor
- Fiddling with a cheap 5 port dumb switch to add VLANs/port mirroring
- Marking intervals in gnuplot graph (with shading)
- The Wifi Doogle
- awk – print text between 2 identical markers in a file
- esp8266 SPI duplex transfers
- A git pre-commit hook to do SVN style $Date$ substitution
- SDG2024x Flash Recovery Files
- SDG800 Reading out flash
- SDG800 recovering from a hosed u-boot
- Hacking around with a SDG800 (SDG805)
- This picture is all wrong
- Sony WPSD5 Surround Sound System “repair” Notes
- A Note On The Ion Torrent Flow Order
- Inside a cheap bubble blowing toy
- Genia’s pore insertion technqiue
- Interfacing Hitachi HD44780 LCDs using I2C on an Arduino
- Notes on Genia’s new paper – nanopore SBS
- PunkSeq10 Schematics and Gerbers
- Are you sure this isn’t horse? – DNA Sequencing is Universal Sensing
- Road to the $1 Genome
- Further Details on the Illumina Firefly
- Personal Genomics Inc./CrackerBio
- A Solexa Story
- Speculation on the Illumina FireFly
- Mitutoyo Digimatic 500-133U CDL-6″B Battery Cover Model
- Notes 16/1/2016
- CX10 Mini Quadcopter 3D Design files
- PunkSeq10 r2
- Thoughts on Writing for Hackaday
- Hobbyist Tech Magazines in Japan
- NEC Teledata Terminal Shop Register (TD7)
- A 1960s Japanese Telephone
- The Repeater – CP-33 Repeat Card Player
- Motorboard – Easydriver/Arduino/PKE243DA interface r1
- Atari Punk Console rev3
- Arduino 8 Channel ADC Board r3
- Veeco Nanoscope V Multimode AFM First Imaging Tests
- Axopatch 200A with micropipette first tests
- Playing with a micropipette puller (Sutter P-97)
- AD5791 Board rev4
- Photodiode array project rev1
- Cracklebox Build Notes
- LEDs as light sensors
- Playing with an Electret Mic
- Photodiode Amplifiers (Transimpedance)
- Scientifica Patchstar
- NEC NP215 DLP Projector Teardown
- AD5791 DAC Arduino shield Rev 3
- LTC1859 ADC Board rev 2
- Atari Punk Console Rev2
- Can Radar Layout
- PI P-915K238 XY Piezo stage
- Inside the Thorlabs MDT690
- SPM Rev2
- Interferometer notes
- Cracklebox rev 2.5
- Krackdoos (Cracklebox) rev2
- SPM Notes (3rd Sept 2015)
- Regulator Board
- +/- 13V Powerboard Rev2
- Couldn’t remount RDWR because of unprocessed orphan inode list. Please umount/remount instead
- Cheap Laser Pointers
- +/- 13V PSU Board Bring up
- Cheap Shenzhen Inspection Microscopes
- AD5791 Board Patches Revisited
- AD5791 Arduino Shield Rev 2
- AD5791 Shield First Rev
- Phonecall From a Scammer
- Atari Punk Console Layout
- LTC1859 8 Channel, 100KSPS +/- 10V 16bit ADC Arduino Shield layout
- Starpack 136 Powersupply
- Surface Pro 3 Charger “Repair”
- Kraakdoos Layout
- Picomotor driver scope traces
- +/- 15V and 5V REF board
- AD5791 Arduino Shield
- AD5791 20Bit DAC Evaluation board with Arduino
- LTC1859CG Evaluation board with an Arduino
- Picomotor 8351 Internal Pics
- Playing with Picomotors
- Cheap Z-stage (SELN LZ-60 Shengling Precise Machinery CO. Ltd)
- Chuo Seiki AMH-13
- Basic bowtie2 alignment notes
- Using BLAST+ for nucleotide alignments
- Interfacing Chuo Seiki stages
- Axopatch 200A Internal Pics
- Lab workbench build notes
- In-place Radix sort O(k) space overhead
- Finding the majority element in a list
- Keyence VE7800 PCB Pics
- Keyence VE7800 Operating Procedure
- esp8266 and kr580vm80a image maps
- Creating LeafletJS tile sets in golang
- Fractal Slippy Map in golang and LeafletJS
- Serving server generated PNGs over HTTP in golang
- Creating a PNG image in golang
- A short review of linear motion
- Vacuum pump types
- Sputtering machine notes
- Imaging of Rice – A review
- Visit to see a SEM (electron microscope)
- Elmo CCD Security camera
- National “TV Camera” Vidicon
- Installing the esp8266 SDK
- Kindlegen, W14001: Hyperlink not resolved errors
- Kohzu linear stages
- Chuo Seiki MMU-60X-H1 XY Stage
- Simple scatter plot in gnuplot
- MPR121 Captouch sensor notes
- MMA7455L 3-axis accelerometer notes
- hp t5325 thin client information and manuals
- HY-DIV268N-5A Stepper driver with Arduino
- Using kindlegen to make a Kindle book
- SEM (Scanning Electron Microscope) Notes
- The Maximum Subarray Problem
- Most common git screwups/questions and solutions
- Select random line from a file in a single pass
- Serving content over HTTPS in golang
- Serving gziped connect via HTTP in golang
- Connect via a SOCKS server in golang
- USRP1 simple data capture in C++ example (UHD)
- ESP8266 – esp1 PCB scans
- Portable electronics toolkit
- Ultra-cheap Chinese Microcontrollers
- Some simple Arduino code to read from a keypad
- Using the Arduino tools from the Linux command line
- Simple JS->DNS Proxy with golang server side
- esp8266 IoT SDK 0.9.5 release, my notes
- Olimex esp8266 PCB Schematics/Layout
- esp8266 analogue input
- esp8266 notes summary
- MSP430Watch2 – Barometer and Wifi (PCB Design)
- BMP180 Barometric Pressure Sensor
- Creating an SVG in Javascript using FabricJS and downloading it locally
- Creating an SVG in Javascript, trivial example
- esp8266 esp1 device programmer gerbers
- Kicad Gerber renaming script for OSHPark (and seeed etc) submission
- esp8266 sleep modes
- Anritsu MT8815b Radio Communication Analyzer Notes
- The esp8266 run loop and messaging
- golang websocket to tcp forwarder
- esp8266 access point mode notes
- Some esp8266 SDK Library symbols
- esp8266 writing to internal flash (basic key/value store)
- Accepting incoming tcp connections on the esp8266 (trivial example)
- esp8266 XBee carrier board PCB design
- esp8266 GPIO input configuration
- esp8266 serial (UART0) tx/rx
- esp8266 wifi doesn’t connect
- esp8266 module types
- A standalone sscanf implementation (for the esp8266)
- Safecast NEMA format notes (bGeigieNano)
- Installing Nagios on Debian Jessie and SNMP (UPS) monitoring
- Posting to the Safecast API from the esp8266
- esp8266 client mode (connect to remote host) simple example
- Paldio パルダイオ 623P
- A Par can stage light notes
- Arduino SNMP Voltage Monitor
- ESP8266 Notes
- Gorilla Websockets, golang simple websockets example
- Getting to awa-kamogawa from Tokyo by train
- Emscripten calling JS from C and returning by reference (pointer)
- Calling JS from C using EM_ASM in Emscripten
- Compiling OpenSSL and libssh2 with emscripten – notes
- Sony/Tektronix 3066 DC-3GHz Realtime spectrum analyzer
- TDS2024 Images
- Very Simple Websocket example in golang
- Typical NPN transistor configurations
- STM vibrational compensation
- Agilent 6624A DC System Power supply
- A 2N2222 die image
- Astable multivibrator RGB flasher PCB design
- The iPhone’s MEMS sensors
- A Common Emitter Hartley Oscillator Notes
- Logitec LBT-VRU01 (bluetooth LE iPhone locator?)
- NPN Common Collector, Colpitts oscillator notes
- Tank Circuits
- NPN BJT Common emitter inverting amplifier
- Simple example of SDL in Emscripten (generating graphics from C)
- Phase Shift Oscillator – High Pass configuration
- Phase Shift Oscillator
- Casio F91W dimensions
- Astable multivibrator oscillator and a little oscillator history
- Electromechanical Oscillator
- C++ convert to/from string
- Asimov on DNA Sequencing
- Simple basic heatmap in D3.JS
- Simple Bar and XY line graph in D3.JS
- Cutting down LCDs
- Driving a tiny stepper on an Arduino (without a driver!)
- Stepper motors notes
- Read a local file into a Javascript string
- Lack of return causes abort() in Emscripten
- Calling C from JS with Emscripten, minimal examples
- Barco OMIX O10 8×11 LED array teardown
- Adding a new program to alternatives manually
- Debian Jessie Emscripten installation notes
- MSP430 with ST7032i, now working!
- An ST7032i on an Arduino Uno
- Union Microscope
- IBM Laptop Supervisor (BIOS) password reset
- STM32-Discovery on Linux
- Slippy maps
- msp430f2013 I2C frustrations
- Inside a 1USD Fingerprint reader
- MSP430 Development on Linux using the eZ430-F2013
- CCD Notes
- Canon Ixy 60 CCD experiments Part 2
- Nginx caching reverse proxy configuration
- Canon Ixy 60 (Powershot SD450)
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About
My name is Nava Whiteford. I’ve worked for a few sequencing companies. I have equity in a few sequencing companies based on my previous employment (I try to be unbiased in my posts). You can contact me at: new@sgenomics.org
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