Pinned Repositories
3DPrintz
A repo to depo all my 3Dprinto
Adafruit-PWM-Servo-Driver-Library
Adafruit PWM Servo Driver Library
AoC
Using google sheets, google script (javascript) to complete. I might do some in Verilog/SystemVerilog and rust as well.
ECE372_I2C2_BBB_NEMA_DRIVER
This project utilizes the Beaglebone Black platform featuring the ARM Cortex-A8 AM335x 1GHZ Sitara Processor. We will be utilizing the I2C2, GPIO, Clock, Timer5, Interrupt Controller peripherals (among others) embedded on the device. BBB GPIO Pin 19 and 20 will be used to interface the I2C2 peripheral output with HW-052 (PCA9685). The HW-052 is a I2C addressable, 16-channel, PWM generating breakout for the PCA9685 IC. It features external driver power delivery and isolated control voltage. The slave address is adjustable via jumpers.
HomeAssistant_stuff
where I am stashing HA scripts
mawLIB
This is a library checkout system for the Resource center that I work in. We deployed it using google sheets. It makes use of scripts, formulas, and web deployed front end.
MobaStripper
When you just need to harvest your MobaXterm passwords but dont have professional.
NPP_GNUARM_OBSIDIAN_CONTRAST
This is a theme for Notepad++ for the GNUARM assembly language theming to contrast the Obsidian theme for NPP.
PSU_ECE586_FinalProject
VRGrove
Arduino sketch and corresponding Unity (C#) code to transfer Grove Trackball data into Unity for the purpose of movement tracking
31415pi's Repositories
31415pi/3DPrintz
A repo to depo all my 3Dprinto
31415pi/HomeAssistant_stuff
where I am stashing HA scripts
31415pi/mawLIB
This is a library checkout system for the Resource center that I work in. We deployed it using google sheets. It makes use of scripts, formulas, and web deployed front end.
31415pi/MobaStripper
When you just need to harvest your MobaXterm passwords but dont have professional.
31415pi/NPP_GNUARM_OBSIDIAN_CONTRAST
This is a theme for Notepad++ for the GNUARM assembly language theming to contrast the Obsidian theme for NPP.
31415pi/PSU_ECE586_FinalProject
31415pi/VRGrove
Arduino sketch and corresponding Unity (C#) code to transfer Grove Trackball data into Unity for the purpose of movement tracking
31415pi/Adafruit-PWM-Servo-Driver-Library
Adafruit PWM Servo Driver Library
31415pi/AoC
Using google sheets, google script (javascript) to complete. I might do some in Verilog/SystemVerilog and rust as well.
31415pi/Assemblies-of-putative-SARS-CoV2-spike-encoding-mRNA-sequences-for-vaccines-BNT-162b2-and-mRNA-1273
RNA vaccines have become a key tool in moving forward through the challenges raised both in the current pandemic and in numerous other public health and medical challenges. With the rollout of vaccines for COVID-19, these synthetic mRNAs have become broadly distributed RNA species in numerous human populations. Despite their ubiquity, sequences are not always available for such RNAs. Standard methods facilitate such sequencing. In this note, we provide experimental sequence information for the RNA components of the initial Moderna (https://pubmed.ncbi.nlm.nih.gov/32756549/) and Pfizer/BioNTech (https://pubmed.ncbi.nlm.nih.gov/33301246/) COVID-19 vaccines, allowing a working assembly of the former and a confirmation of previously reported sequence information for the latter RNA. Sharing of sequence information for broadly used therapeutics has the benefit of allowing any researchers or clinicians using sequencing approaches to rapidly identify such sequences as therapeutic-derived rather than host or infectious in origin. For this work, RNAs were obtained as discards from the small portions of vaccine doses that remained in vials after immunization; such portions would have been required to be otherwise discarded and were analyzed under FDA authorization for research use. To obtain the small amounts of RNA needed for characterization, vaccine remnants were phenol-chloroform extracted using TRIzol Reagent (Invitrogen), with intactness assessed by Agilent 2100 Bioanalyzer before and after extraction. Although our analysis mainly focused on RNAs obtained as soon as possible following discard, we also analyzed samples which had been refrigerated (~4 ℃) for up to 42 days with and without the addition of EDTA. Interestingly a substantial fraction of the RNA remained intact in these preparations. We note that the formulation of the vaccines includes numerous key chemical components which are quite possibly unstable under these conditions-- so these data certainly do not suggest that the vaccine as a biological agent is stable. But it is of interest that chemical stability of RNA itself is not sufficient to preclude eventual development of vaccines with a much less involved cold-chain storage and transportation. For further analysis, the initial RNAs were fragmented by heating to 94℃, primed with a random hexamer-tailed adaptor, amplified through a template-switch protocol (Takara SMARTerer Stranded RNA-seq kit), and sequenced using a MiSeq instrument (Illumina) with paired end 78-per end sequencing. As a reference material in specific assays, we included RNA of known concentration and sequence (from bacteriophage MS2). From these data, we obtained partial information on strandedness and a set of segments that could be used for assembly. This was particularly useful for the Moderna vaccine, for which the original vaccine RNA sequence was not available at the time our study was carried out. Contigs encoding full-length spikes were assembled from the Moderna and Pfizer datasets. The Pfizer/BioNTech data [Figure 1] verified the reported sequence for that vaccine (https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/), while the Moderna sequence [Figure 2] could not be checked against a published reference. RNA preparations lacking dsRNA are desirable in generating vaccine formulations as these will minimize an otherwise dramatic biological (and nonspecific) response that vertebrates have to double stranded character in RNA (https://www.nature.com/articles/nrd.2017.243). In the sequence data that we analyzed, we found that the vast majority of reads were from the expected sense strand. In addition, the minority of antisense reads appeared different from sense reads in lacking the characteristic extensions expected from the template switching protocol. Examining only the reads with an evident template switch (as an indicator for strand-of-origin), we observed that both vaccines overwhelmingly yielded sense reads (>99.99%). Independent sequencing assays and other experimental measurements are ongoing and will be needed to determine whether this template-switched sense read fraction in the SmarterSeq protocol indeed represents the actual dsRNA content in the original material. This work provides an initial assessment of two RNAs that are now a part of the human ecosystem and that are likely to appear in numerous other high throughput RNA-seq studies in which a fraction of the individuals may have previously been vaccinated. ProtoAcknowledgements: Thanks to our colleagues for help and suggestions (Nimit Jain, Emily Greenwald, Lamia Wahba, William Wang, Amisha Kumar, Sameer Sundrani, David Lipman, Bijoyita Roy). Figure 1: Spike-encoding contig assembled from BioNTech/Pfizer BNT-162b2 vaccine. Although the full coding region is included, the nature of the methodology used for sequencing and assembly is such that the assembled contig could lack some sequence from the ends of the RNA. Within the assembled sequence, this hypothetical sequence shows a perfect match to the corresponding sequence from documents available online derived from manufacturer communications with the World Health Organization [as reported by https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/]. The 5’ end for the assembly matches the start site noted in these documents, while the read-based assembly lacks an interrupted polyA tail (A30(GCATATGACT)A70) that is expected to be present in the mRNA.
31415pi/ECE372_I2C2_BBB_NEMA_DRIVER
This project utilizes the Beaglebone Black platform featuring the ARM Cortex-A8 AM335x 1GHZ Sitara Processor. We will be utilizing the I2C2, GPIO, Clock, Timer5, Interrupt Controller peripherals (among others) embedded on the device. BBB GPIO Pin 19 and 20 will be used to interface the I2C2 peripheral output with HW-052 (PCA9685). The HW-052 is a I2C addressable, 16-channel, PWM generating breakout for the PCA9685 IC. It features external driver power delivery and isolated control voltage. The slave address is adjustable via jumpers.
31415pi/autosub
[NO LONGER MAINTAINED] Command-line utility for auto-generating subtitles for any video file
31415pi/CATS_Combsmaster_CTF
Hacking md5 on the bots entry system for the fall 2020 PSU CATS CTF
31415pi/ECE_411_Winter_2021_Team_7
Group project for 411
31415pi/EPL-RFID
RFID system for controlling access to EPL machines
31415pi/F0_mawlzzdev
Flipper Zero Code-Grabber Firmware
31415pi/Finances_Workbook
31415pi/FlipperZeroHeaderExtender_plus
Flipper Zero Header Extender Gerber Files -- adding modifications here
31415pi/FragEvade
31415pi/HROS5-Framework
HR-OS5 Framework, based on the Darwin-OP project. Intended for use on HR-OS5 Research Humanoid Robot platforms.
31415pi/KomfiBot
A discord bot integrating ComfyUI Image generation workflow to generate from user prompts
31415pi/Limnoria
A modified version of Supybot (an IRC bot) with Python 3 and IRCv3 support including SASL, translations (fr/fi/it/hu/de), GPG authentication, TLS, and many other enhancements and bug fixes
31415pi/PiHoleBlocklist
PiHole and AGH Blocklists
31415pi/PSU_ECE485_585_Group_14_Project_Memorystars
31415pi/PSU_S3_2022_Cohort_RPi4_Cat_Pew_tracker
Final Project for 2022 Cohort of the S3 program at PSU - Laser pointer controller which implements OpenCV to track a cat and tease it with a laser pointer.
31415pi/ratchetHatchet
Development drop zone for hacking the Ratchet Eurorack Module by Schottkey
31415pi/Repo_Accumulator
31415pi/Spring21_MCECS
31415pi/Summer_2021
PSU Summer 2021 course HW and etc.
31415pi/webscraper_chrome_ext
Metadata saves for chrome extension Web Scraper