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If you are wondering where the data of this site comes from, please visit https://api.github.com/users/davidkuhta/events. GitMemory does not store any data, but only uses NGINX to cache data for a period of time. The idea behind GitMemory is simply to give users a better reading experience.
David Kuhta davidkuhta AI/ML Software Engineer

davidkuhta/fuentes 23

:ledger: A double-entry accounting package for Elixir using Ecto

davidkuhta/dasc2 3

StarCraft II Data Analytics

davidkuhta/GraphVR 1

A repository of tools for exploring graphs in virtual environments utilizing the Oculus Rift and Unreal Engine 4.

davidkuhta/arc 0

:paperclip: Flexible file upload and attachment library for Elixir

davidkuhta/arc_ecto 0

An integration with Arc and Ecto.

davidkuhta/asdf 0

Extendable version manager with support for Ruby, Node.js, Elixir, Erlang & more

davidkuhta/Assemblies-of-putative-SARS-CoV2-spike-encoding-mRNA-sequences-for-vaccines-BNT-162b2-and-mRNA-1273 0

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.

davidkuhta/bamboo 0

Testable, composable, and adapter based Elixir email library for devs that love piping.

davidkuhta/Birdsong 0

:bird::musical_score: Swift WebSockets client for Phoenix Channels.

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Gregory Essertel

commit sha dee3b11db45ead77a3bd5255790afee355607366

simpler code

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Gregory Essertel

commit sha 0f4b8957b46ccabf1ad02e4874740eb146caf6fb

better key/value

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PR opened strateos/transcriptic

feature: add filtering of instructions on the exec command

Summary:

Add a --exclude/-e and --include/-i flags on the exec command to filter instructions.

Usage:

cat autoprotocol.json | transcriptic exec -a lab.core.strateos.com/haven/wctest -w wc4-mcx1 -e 1-9 -i 7 -e op:provision

This command will first filter out instruction from index 1 to 9 (-e 1-9) and the provisions (-e op:provision). Then add back the instruction at index 7 (-i 7).

The order of -i/-e don't matter, it is first removing all the -e, then adding back all the -i.

Possible filter:

  • single index: 123
  • range: 123-456
  • key:value in the instruction: op:provision, or x_human!:false. The ! means that if the key (x_human) is not in the instruction, then the filter matches. Otherwise, without the '!' a missing key means that there is no match.

Example:

  • { "op": "seal", "x_human": false } and { "op": "seal" } match x_human!:false
  • { "op": "seal" } does not matchx_human:true, nor x_human:false
+266 -19

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Gregory Essertel

commit sha 033143cc7e9fc390ce26e0f12f09dc2299f4230f

Add human filter

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branch : GE-add-filter-flag

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pull request commentlervag/vimtex

doc: Add nvim-compe to the autocompletion section

Ok, thanks. If something like that should be implemented, then feel free to notify me and/or suggest an update to the configuration suggestions in the docs.

savq

comment created time in 2 hours

issue closedlervag/vimtex

Table of Contents removes alternate file

Opening Vimtex's Table of Contents removes Vim's alternate file.

  1. Edit the file below.

  2. Compile to create highlight.bib.

  3. e highlight.bib to open an alternate file.

  4. ctrl-^ three times to switch back to the .tex file and forth and back again.

  5. <local-leader>lt to open the TOC.

  6. ctrl-^ to switch to the alternate file.

    "E23: No alternate file"

This behavior doesn't occur with Vundle's PlugInList, which similarly opens a new buffer in a split. The alternate file is retained after closing the split.

\documentclass{article}
\usepackage[style=verbose-ibid]{biblatex}
\addbibresource{highlight.bib}

\begin{filecontents}{highlight.bib}

@book{Hemingway:For_Whom_the,
	author   = {Earnest Hemingway},
	title    = {For Whom the Bell Tolls},
	date     = {1940},
	publisher  = {Simon \& Schuster},
}

\end{filecontents}

\begin{document}

\section{Introduction}

Some text here.\autocite[10]{Hemingway:For_Whom_the}

\end{document}

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bongbang

issue commentlervag/vimtex

Table of Contents removes alternate file

Thanks, I think this should be fixed now.

bongbang

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Karl Yngve Lervåg

commit sha 1f0fe03d0e2799d34520852d6d026acb700dbf05

fix: minor adjustment of bib parser

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Karl Yngve Lervåg

commit sha 6c0c94e985fd0c46dff92205ad3ac661bf82e3a6

fix: restore alternate buffer after ToC use refer: #2073

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pull request commentlervag/vimtex

doc: Add nvim-compe to the autocompletion section

One open question remains: Is there something in nvim-compe that is equivalent to the input_patterns variable in deoplete/neocomplete, or the complete_pattern in ncm2?

@lervag, compe seems to be able to use regex patterns for the buffer source, but not for omni-completion. The default pattern matches alphanumeric words, including kebab-case: \h\w*\%(-\w*\)*. The docs mention it's an experimental feature.

savq

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create barnchs-gv/orangeforum

branch : sagar/multi-domain

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fork dusty-nv/py3gazebo

Python bindings for the Gazebo multi-robot simulator.

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Sagar Gubbi

commit sha bf74b04616fbd375087c29e2ec96299a07644e1a

Super user creation from command line

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Sagar Gubbi

commit sha c5e17eaec8e11ea9bcf8305c5e1a370abd2394fd

Basic DB migration setup

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Sagar Gubbi

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Management commands for command line user and domain creation

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PR merged s-gv/orangeforum

Sagar/user auth
+304 -24

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s-gv

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PR opened s-gv/orangeforum

Sagar/user auth
+304 -24

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Sagar Gubbi

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Management commands for command line user and domain creation

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Sagar Gubbi

commit sha 0f9a7f09d4de5a9946c4bac71c85dc8c751bfc01

Management commands for command line user and domain creation

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startedibraheemdev/modern-unix

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Sagar Gubbi

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Basic DB migration setup

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issue commentbabybuddy/babybuddy

Potential security issue

@cdubz - no worries, feel free to confirm a fix once you feel the vuln is patched!

oomb

comment created time in 8 hours

issue commentbabybuddy/babybuddy

Potential security issue

Thanks @oomb and @JamieSlome -- POC works as described and I have marked this issue as valid.

oomb

comment created time in 9 hours

issue openedabsinthe-graphql/absinthe

`mix clean` is sometimes required to see changes take effect

Environment

  • Elixir version (elixir -v): Erlang/OTP 23 [erts-11.2] [source] [64-bit] [smp:12:12] [ds:12:12:10] [async-threads:1] [hipe]
  • Absinthe version (mix deps | grep absinthe): absinthe 1.6.4 / absinthe_plug 1.5.8
  • Client Framework and version (Relay, Apollo, etc): graphiql

Expected behavior

Changing my types file from field(:id, :id) to field :id, :string do resolve(fn object, _, _ -> {:ok, GlobalId.encode(Spiff.Comment, object.id)} end) end

Sometimes does not register as a change

Actual behavior

id continued to behave as a plain db column until I ran mix clean and restarted. Then it works as expected. Restarting iex on its own is not enough to break the stale cache.

created time in 9 hours

issue openedlervag/vimtex

Table of Contents removes alternate file

Opening Vimtex's Table of Contents removes Vim's alternate file.

  1. Edit the file below.
  2. Compile to create highlight.bib.
  3. e highlight.bib to open an alternate file.
  4. ctrl-^ three times to switch back to the .tex file and forth and back again.
  5. <local-leader>lt to open the TOC.
  6. ctrl-^ to switch to the alternate file.

"E23: No alternate file"

This behavior doesn't occur with Vundle's PlugInList, which similarly opens a new buffer in a split. The alternate file is retained after closing the split.

\documentclass{article}
\usepackage[style=verbose-ibid]{biblatex}
\addbibresource{highlight.bib}

\begin{filecontents}{highlight.bib}

@book{Hemingway:For_Whom_the,
	author   = {Earnest Hemingway},
	title    = {For Whom the Bell Tolls},
	date     = {1940},
	publisher  = {Simon \& Schuster},
}

\end{filecontents}

\begin{document}

\section{Introduction}

Some text here.\autocite[10]{Hemingway:For_Whom_the}


\end{document}

created time in 10 hours

issue commentbabybuddy/babybuddy

Potential security issue

@cdubz - you should now have access to the report!

Apologies for that! ❤️

oomb

comment created time in 10 hours

PR merged lervag/vimtex

doc: Add nvim-compe to the autocompletion section

Following this reddit thread, this PR adds some information on how to use VimTeX with nvim-compe.

I didn't find info on whether compe can use regex patterns for filetypes 😕 but I followed u/mybumsonfire advice on adding the filetype explicitly.

I added a code sample in Lua, though another one in Vimscript can also be added.

I'm glad VimTeX is so well documented 👍

+26 -5

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savq

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Sergio Alejandro Vargas

commit sha a0acaaf9cd3099c9fea260795557fb327866be65

doc: Add nvim-compe to the autocompletion section

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Karl Yngve Lervåg

commit sha b9361cf887a5fac633c787bad7cce5a51ca80534

doc: minor adjustments

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Karl Yngve Lervåg

commit sha 5d852e7a60d63f56eb30062c946d045042aa68ed

merge: document autocompleter nvim-compe refer: #2072

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pull request commentlervag/vimtex

doc: Add nvim-compe to the autocompletion section

Following this reddit thread, this PR adds some information on how to use VimTeX with nvim-compe.

Thank you!

I'm glad VimTeX is so well documented +1

Yes, I think it's important to aim for good documentation, especially considering the size of the plugin. And help from people like you is therefore very useful!

I am writing just to confirm that @savq has provided the correct config (which the original reddit post is not).

Thanks! Also thanks for the references to relevant issues!


One open question remains: Is there something in nvim-compe that is equivalent to the input_patterns variable in deoplete/neocomplete, or the complete_pattern in ncm2?

savq

comment created time in 11 hours

issue commentbabybuddy/babybuddy

Potential security issue

:wave: @oomb -- thanks for the report. I have never used huntr before and can't seem to get it to recognize me as the maintainer to confirm. I authed with GH but still see the "If you're the maintainer, login to view the report." and if I click it it just dead ends on a black screen.

oomb

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