Tag: SRC

CIBERSORTxFractions ERROR: Could not read /src/outdir//temp.Fractions.simfracs.tsv

Hello, can anyone offer any insight into the following problem? I am trying to run the following CIBERSORTx function locally: docker run -v /media/mark/seagate2/data/CIBERSORTx_GC:/src/data -v /media/mark/seagate2/data/CIBERSORTx_GC:/src/outdir cibersortx/fractions –username <my_user_name> –token <my_token> –single_cell TRUE –refsample reference.txt –mixture rsem_mixture_TPM.tsv –fraction 0 –rmbatchSmode TRUE I get the following output to the terminal: >Running…

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log repeats until it times out)

Your message dated Sat, 22 Jan 2022 21:52:05 +0100 with message-id <f98ce279-5828-d2b5-8b7c-88287a3ab…@debian.org> and subject line Re: Bug#997845: bug 997845 has caused the Debian Bug report #997845, regarding growlight: autopkgtest regression: log repeats until it times out to be marked as done. This means that you claim that the problem has…

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Pair_write with eam/alloy – error – LAMMPS General Discussion

Dear LAMMPS Users, I encountered a problem while trying to use pair_write command with an eam/alloy potential. pair_style hybrid eam/alloy table spline 100000 zbl 1.0 4.0pair_coeff * * eam/alloy Be_Agrawal.eam.alloy Be NULLpair_coeff 1 2 table DBe.potential-table DFT_DBEpair_coeff 2 2 zbl 1.0 1.0pair_write 1 1 100 r 1.0 6.0 table.txt metal…

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Adding ions ‘gmx grompp’ creates error “Atomtype ca not found” for ligand generated with GAFF – User discussions

GROMACS version: 2018GROMACS modification: No Hello, I am trying to run 200ns on protein-ligand complex and then calculate MMPBSA for the last 100 ns generated frames. I had some problems with ligand parameterization with cgenff, hence I used gaff…I have: GAFF to generate parameters for the ligand acpype to convert…

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MySQL always no result – Discussion

So I’ve been trying to create a custom system (kinda lika a garage system, but different) for my server.As I got to the part where I display the player all vehicles he ownes I need to create a server callback where the script gets all vehicles from the database using…

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Gst-nvivafilter – Jetson AGX Xavier

Platforms: Jetson AGX Xavier Jetpack 4.5 Cuda 10.2 IMX274 camera Hi fellow developers, I am having difficulties at making custom CUDA implementation. I have succesfully run the below pipeline. gst-launch-1.0 nvarguscamerasrc ! ‘video/x-raw(memory:NVMM), width=(int)3840, height=(int)2160, format=(string)NV12, framerate=(fraction)60/1’ ! nvivafilter cuda-process=true customer-lib-name=”libnvsample_cudaprocess.so” ! ‘video/x-raw(memory:NVMM), format=(string)NV12’ ! nvvidconv ! nvegltransform ! nveglglessink…

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Coul MSM – Segmentation Fault – LAMMPS Development

Without root access you cannot install gdb or valgrind from a package repository, but you can still install them by compiling from source. It is not too difficult, especially gdb. It just takes a little time. But the gdb information can make up for the time invested quickly. Please note…

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Cannot install Phyloseq and dada2

Hello all, I have been having issues installing packages that I really need to use. Basically, I cannot download either Phyloseq or dada2 and I believe it’s because I don’t have GenomeInfoDbData. But at the same time, I cannot install GenomeInfoDbData because I can’t seem to update the dependencies (“fansi”…

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gromacs 2021.5 – Download, Browsing & More

gromacs 2021.5 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of gromacs-2021.5.tar.gz (14 Jan 16:58, 38023772 Bytes) About: GROMACS performs molecular dynamics, i.e. simulates the Newtonian equations of motion for systems with hundreds to millions of particles (designed for biochemical molecules…

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traviz 1.0.0 installation fails: ERROR: lazy loading failed

Hi, I cannot install traviz package (version 1.0.0) from Bioconductor on a linux machine (from source). I have a conda environment, and I installed traviz from conda, but it cannot be used – when I do library(traviz) R just crashes and quits without any message. So I tried to install…

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R connection to sqlite – Stackify

SQLite is a file level database, hence to reference it requires a full directory path. No where do you specify the working directory or a full path in the file name. By default, R will use the current working directory contained in getwd(). If database is not contained in this…

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scikit-survival | Zenodo

Zenodo DOI Badge DOI 10.5281/zenodo.5831584 Markdown [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5831584.svg)](https://doi.org/10.5281/zenodo.5831584) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.5831584.svg :target: doi.org/10.5281/zenodo.5831584 HTML <a href=”https://doi.org/10.5281/zenodo.5831584″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.5831584.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.5831584.svg Target URL doi.org/10.5281/zenodo.5831584 Read more here: Source link

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python – Where to upload the image files to JupyterHub server (ltjh)

I would like to create a jupyter notebook that displays some images like this. In the case of my computer, the image files are stored in the local device. So I wrote one-line tag to show the image. <img src=”images/python_with_Birds.gif” width=”400″/> But if I want to share my created jupyter…

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intermine/intermine: InterMine 5.0.6 | Zenodo

Zenodo DOI Badge DOI 10.5281/zenodo.5827966 Markdown [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5827966.svg)](https://doi.org/10.5281/zenodo.5827966) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.5827966.svg :target: doi.org/10.5281/zenodo.5827966 HTML <a href=”https://doi.org/10.5281/zenodo.5827966″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.5827966.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.5827966.svg Target URL doi.org/10.5281/zenodo.5827966 Read more here: Source link

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make Pyspark working inside jupyterhub

You need to configure the pyspark kernel. On my server jupyter kernels are located at: /usr/local/share/jupyter/kernels/ You can create a new kernel by making a new directory: mkdir /usr/local/share/jupyter/kernels/pyspark Then create the kernel.json file – I paste my as a reference: { “display_name”: “pySpark (Spark 1.6.0)”, “language”: “python”, “argv”: […

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Processed: src:pktanon: fails to migrate to testing for too long: autopkgtest regression on armhf

Processing control commands: > close -1 2~git20160407.0.2bde4f2+dfsg-8 Bug #1003104 [src:pktanon] src:pktanon: fails to migrate to testing for too long: autopkgtest regression on armhf Marked as fixed in versions pktanon/2~git20160407.0.2bde4f2+dfsg-8. Bug #1003104 [src:pktanon] src:pktanon: fails to migrate to testing for too long: autopkgtest regression on armhf Marked Bug as done >…

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Index of /~psgendb/doc/pkg/last/src

Name Last modified Size Description Parent Directory   –   Alignment.cc 2021-04-13 03:43 16K   Alignment.hh 2021-04-13 03:43 7.0K   AlignmentPot.cc 2021-04-13 03:43 703   AlignmentPot.hh 2021-04-13 03:43 2.1K   AlignmentWrite.cc 2021-04-13 03:43 22K   Alphabet.cc 2021-04-13 03:43 3.6K   Alphabet.hh 2021-04-13 03:43 2.3K   Centroid.cc 2021-04-13 03:43 20K  …

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Lammps in wsl – LAMMPS Installation

after making ubuntu in windows and installing the prerequisite commands ( sudo apt install -y cmake build-essential ccache gfortran openmpi-bin libopenmpi-dev libfftw3-dev libjpeg-dev libpng-dev python3-dev python3-pip python3-virtualenv libblas-dev liblapack-dev libhdf5-serial-dev hdf5-tool)I downloadedLAMMPS Patch Release 14 Dec 2021 From www.lammps.org/download.htmland after extracting, I put it on the desktop. Next I entered…

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r markdown – Cant get r code to run in kaggle notebook

So I’m competing in the NFL Big Data Bowl hosted by Kaggle and I’m having trouble uploading both r script and rmd into kaggle. I keep getting parse errors that I can’t seem to get around. I’ve even tried copy pasting code from other peoples code from similar notebooks but…

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Bug#1003017: dulwich: autopkgtest regression: src/debian/tests/testsuite3: 10: -m: not found

Source: dulwich Version: 0.20.26-1 X-Debbugs-CC: debian…@lists.debian.org Severity: serious User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of dulwich the autopkgtest of dulwich fails in testing when that autopkgtest is run with the binary packages of dulwich from unstable. It passes when run with only packages from testing. In…

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Tensorflow realizes kaggle cat and dog recognition (network design step by step)

This article is tensorflow edition ,pytorch The version will be given in the next blog Friendship tips : Try GPU, Blogger CPU Run on one VGG16 It took 1.5h… Tensorflow Realization kaggle Cat and dog recognition Online disk download link :pan.baidu.com/s/1kqfkr2X7mMkuFXb6C3KgTgExtraction code :xzyh kaggle Download it on the official website…

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MOLECULE package – LAMMPS Installation

Dear LAMMPS users, I want to run a LAMMPS simulation using HPC that include the Linux version of LAMMPS (14 Dec 2021), but I face the below error just after running the simulation: ERROR: Unrecognized atom style ‘full’ is part of the MOLECULE package which is not enabled in this…

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[Buildroot] [PATCH 1/2] package/mbedtls3: new package

[Buildroot] [PATCH 1/2] package/mbedtls3: new package * [Buildroot] [PATCH 1/2] package/mbedtls3: new package @ 2021-12-28 15:33 Fabrice Fontaine 2021-12-28 15:33 ` [Buildroot] [PATCH 2/2] package/hiawatha: needs mbedtls3 Fabrice Fontaine 2021-12-28 15:49 ` [Buildroot] [PATCH 1/2] package/mbedtls3: new package Thomas Petazzoni 0 siblings, 2 replies; 5+ messages in thread From: Fabrice…

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SageMath Cells ans CSS – githubmate

In the embedded SageMath Cells (see for instance mathifold.org/en/applet_hyperbolic_tessellations.html), the editor is currently hidden {% if page.sage %} <script src=”https://sagecell.sagemath.org/static/embedded_sagecell.js”></script> <script>$(function () { // Make *any* div with class ‘compute’ a Sage cell sagecell.makeSagecell({inputLocation: ‘div.sage’, hide: [“editor”, “evalButton”, “permalink”], autoeval: 1}); }); </script> {% endif %} (github.com/mathifold/mathifold/blob/master/_includes/head.html). However, it is…

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How do I “flush” data to my RSQLite disk database?

You’re not using the pattern suggested by the RSQLite documentation. That documentation uses dbWriteTable to copy a data frame into a SQLite table: dbWriteTable(con, “mtcars”, mtcars) According to this documentation, your full code would look something like this: con <- dbConnect(RSQLite::SQLite(), “./mtcars.db”) data(mtcars) dbWriteTable(con, “mtcars”, mtcars) dbListTables(con) # Fetch all…

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sqldf : create table from data frame error: “no such table”. and two tables created instead of one

UPDATE: newest versions of RSQLite and sqldf do not have the incompatibility issues addressed by this question i.e.: sqldf_0.4-10 RSQLite_1.1-2 work together well – Nathan All: Thanks to G. Grothendieck for pointers to incompatibility issues introduced by RSQLite 1.1-1. As stated in the comment to the answer, downgrade RSQLite to…

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LAMMPS failed to install with Intel compiler due to cpio and diffutils

$ spack install lammps%intel +asphere +class2 +kspace +manybody +misc +molecule +mpiio +opt +replica +rigid +user-omp +user-intel ^intel-mkl ^intel-mpi (base) bash-4.2$ spack install lammps%intel +asphere +class2 +kspace +manybody +misc +molecule +mpiio +opt +replica +rigid +user-omp +user-intel ^intel-mkl ^intel-mpi [+] /opt/intel/cmake (external cmake-3.20.0-3teotjsa6webcsazofydfkk2v3pn2hb6) [+] /nfs/pdx/home/sdouyeb/spack/opt/spack/linux-centos7-skylake_avx512/intel-19.1.3.304/alsa-lib-1.2.3.2-yctbppr2tcdayclbt32xjgagmmwbct2v [+] /nfs/pdx/home/sdouyeb/spack/opt/spack/linux-centos7-skylake_avx512/intel-19.1.3.304/libiconv-1.16-ilxedtsoqggtmtbrjxehh6ojznmtdni3 [+] /nfs/pdx/home/sdouyeb/spack/opt/spack/linux-centos7-skylake_avx512/intel-19.1.3.304/yasm-1.3.0-7y4fvxshqkmikii3cvelccaiajj4dboc [+] /nfs/pdx/home/sdouyeb/spack/opt/spack/linux-centos7-skylake_avx512/intel-19.1.3.304/zlib-1.2.11-k24vg36ubsrvwfgrdipndmpqn4eo5jq7 ==>…

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kojix2/ruby-htslib: v0.0.4 | Zenodo

Zenodo DOI Badge DOI 10.5281/zenodo.5797825 Markdown [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5797825.svg)](https://doi.org/10.5281/zenodo.5797825) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.5797825.svg :target: doi.org/10.5281/zenodo.5797825 HTML <a href=”https://doi.org/10.5281/zenodo.5797825″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.5797825.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.5797825.svg Target URL doi.org/10.5281/zenodo.5797825 Read more here: Source link

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r – RSQLite Error “hash is not an exported object”

I am trying to scrape some pitchf/x data and store it in an SQLite database. However, I am receiving the following error when I run the following code: library(RSQLite) library(dplyr) db <- src_sqlite(“pitchfx.sqlite3”, create = T) This is the error: Error in h(simpleError(msg, call)) : error in evaluating the argument…

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Bioinformatics Engineer – Idealist

POSITION SUMMARY The Simons Foundation is seeking a Bioinformatics/Senior Bioinformatics Engineer (dependant upon experience) to develop and support whole exome and genome sequence data analysis pipelines in both research and operational modalities. This position will report to the Director of Data and Analytics in the informatics group and will work…

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bioinformatics – Local BLAST NCBI C++ Exception

I’m getting an error trying to to use blast v2.12 against a local nt database. I’ve downloaded nt twice from the ftp server thinking the first time it was corrupt but that didn’t change anything. My command is: blastn -db nt -num_threads 8 -outfmt “6 qseqid sacc stitle ssciname nident…

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Gromacs: src/gromacs/gmxpreprocess Directory Reference

Directory dependency graph for gmxpreprocess: This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. Directories directory   tests   Files file   add_par.c   file   add_par.h   file   calch.c   file   calch.h   file   convparm.c   file   convparm.h  …

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#1001716 – src:minimap2: fails to migrate to testing for too long: autopkgtest regression

#1001716 – src:minimap2: fails to migrate to testing for too long: autopkgtest regression – Debian Bug report logs Reported by: Paul Gevers <elbrus@debian.org> Date: Tue, 14 Dec 2021 20:03:02 UTC Severity: serious Tags: bookworm, sid Found in version minimap2/2.17+dfsg-12 Fixed in version minimap2/2.22+dfsg-3 Done: Paul Gevers <elbrus@debian.org> Reply or subscribe…

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Bug#1001735: node-trust-keyto: autopkgtest regression: Cannot find module ‘@trust/keyto’

Source: node-trust-keyto Version: 2.0.0~alpha1-1 X-Debbugs-CC: debian…@lists.debian.org Severity: serious User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of node-trust-keyto the autopkgtest of node-trust-keyto fails in testing when that autopkgtest is run with the binary packages of node-trust-keyto from unstable. It passes when run with only packages from testing. In…

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Bug#1001716: src:minimap2: fails to migrate to testing for too long: autopkgtest regression

Source: minimap2 Version: 2.17+dfsg-12 Severity: serious Control: close -1 2.22+dfsg-3 Tags: sid bookworm User: release.debian….@packages.debian.org Usertags: out-of-sync Dear maintainer(s), The Release Team considers packages that are out-of-sync between testing and unstable for more than 60 days as having a Release Critical bug in testing [1]. Your package src:minimap2 has been…

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[BUG] (python-fastapi) OneOf class not generated

Bug Report Checklist Description For oneOf fields, the python-fastapi server generator creates a function that returns a OneOf* class, but that class itself is not generated. For example, for an API like /status: get: summary: Get the status of the upstream server responses: 200: description: successful operation content: application/json: schema:…

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FTBFS on riscv64, linked with -lpthread instead of -pthread

Package: fastp Version: 0.23.2+dfsg-1 Severity: normal Tags: ftbfs upstream patch User: debian-ri…@lists.debian.org Usertags: riscv64 Dear maintainer, fastp currently fails to build from source on riscv64: | g++ ./obj/adaptertrimmer.o ./obj/basecorrector.o ./obj/duplicate.o ./obj/evaluator.o ./obj/fastareader.o ./obj/fastqreader.o ./obj/filter.o ./obj/filterresult.o ./obj/htmlreporter.o ./obj/jsonreporter.o ./obj/main.o ./obj/nucleotidetree.o ./obj/options.o ./obj/overlapanalysis.o ./obj/peprocessor.o ./obj/polyx.o ./obj/processor.o ./obj/read.o ./obj/readpool.o ./obj/seprocessor.o ./obj/sequence.o ./obj/stats.o ./obj/threadconfig.o…

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Gromacs: gmx::LastStepSignaller Class Reference

#include <gromacs/modularsimulator/signallers.h> Inheritance diagram for gmx::LastStepSignaller: This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. [legend] Collaboration diagram for gmx::LastStepSignaller: This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. [legend] Description Element signalling the last step. This element…

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python – How does one install PyTorch and related tools from within the setup.py install_requires list?

I was trying to test the pip install -e . on my library ultimate-utils after changing laptops but I keep getting errors of this type: (uutils_env) brandomiranda~/ultimate-utils ❯ pip install -e . Obtaining file:///Users/brandomiranda/ultimate-utils Preparing metadata (setup.py) … done ERROR: Could not find a version that satisfies the requirement torchvision==0.10.1…

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TRON-Bioinformatics/tronflow-bam-preprocessing: Release v1.7.1 | Zenodo

Zenodo DOI Badge DOI 10.5281/zenodo.5768626 Markdown [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5768626.svg)](https://doi.org/10.5281/zenodo.5768626) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.5768626.svg :target: doi.org/10.5281/zenodo.5768626 HTML <a href=”https://doi.org/10.5281/zenodo.5768626″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.5768626.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.5768626.svg Target URL doi.org/10.5281/zenodo.5768626 Read more here: Source link

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Couldn’t load the Pytorch optimised model in android

This is the error I’m getting in android while loading the model. java.lang.RuntimeException: Unable to start activity ComponentInfo{com.android.example.cataractdetectionapp/com.android.example.cataractdetectionapp.InferenceActivity}: com.facebook.jni.CppException: Could not run ‘aten::empty_strided’ with arguments from the ‘CUDA’ backend. This could be because the operator doesn’t exist for this backend, or was omitted during the selective/custom build process (if using…

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How to remove ApiUtil.java from openApi geneate task with openapi-generator-gradle-plugin:4.3.0

I have am using openapi-generator-gradle-plugin:4.3.0 to generate the api and models from a openApi-generate.yaml file. I have set skipDefaultInterface: “true” in configOptions, the default implementation of interfaces is not generated and ApiUtil.java is not used anywhere. (The default implementations used ApiUtil.java) What I want is to remove (disable the generation…

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Does PyTorch plan to support “Cpp-like” round? – #5 by Eta_C

round in PyTorch is a “Python-like” round (std::nearbyint) but not a “Cpp-like” round (std::round). It means, round([-0.5, 0.5]) would return [0, 0] but not [-1, 1]. I need “Cpp-like” round, especially when deploying my model. I check the source code and find github.com pytorch/pytorch/blob/178010455d5cd477af5a98b0e03084ffeecaecf2/aten/src/ATen/cpu/vec/vec_base.h#L469-L471 Vectorized<T> round() const { // We…

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main-arm64-default][devel/RStudio] Failed for RStudio-2021.09.1+372 in build

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: ampere2.nyi.freebsd.org/data/main-arm64-default/p7539e33f88ff_s169b368a62/logs/RStudio-2021.09.1+372.log Build URL: ampere2.nyi.freebsd.org/build.html?mastername=main-arm64-default&build=p7539e33f88ff_s169b368a62 Log: =>> Building devel/RStudio build started at Wed Dec 8…

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How to open file from JupyterHub workspace when using %%javascript magic?

I use JupyterHub in combination with JupyterLab. I have a user “test” and a file “data.csv” in the workspace of that user. I would like to use %%javascript magic and load that file with d3.js. However, the url “./data.csv” does not work. =>What is the right relative url to load…

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Bioconductor URI, fallback and time-machine

Hi,On Tue, 03 Mar 2020 at 16:59, zimoun <zimon.toutoune@gmail.com> wrote: Toggle quote (17 lines) > Currently, the URI scheme (see ‘bioconductor-uri’ in> guix/build-system/r.scm) is:>> bioconductor.org/packages/release/data/<type-url-part>/src/contrib/<upstream-name>-<version&gt;.tar.gz>> which leads to 2 issues:>> 1. when Bioconductor updates their release, some package versions are> updated too, and so, the upstream return 404.> 2. for…

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lammps_helper | Read the Docs

Repository github.com/kevinwhitham/lammps_helper.git Project Slug lammps-helper Last Built 1 year ago passed Maintainers Badge reStructuredText .. image:: readthedocs.org/projects/lammps-helper/badge/?version=latest :target: lammps-helper.readthedocs.io/en/latest/?badge=latest :alt: Documentation Status Markdown [![Documentation Status](https://readthedocs.org/projects/lammps-helper/badge/?version=latest)](https://lammps-helper.readthedocs.io/en/latest/?badge=latest) HTML <a href=”https://lammps-helper.readthedocs.io/en/latest/?badge=latest”> <img src=”https://readthedocs.org/projects/lammps-helper/badge/?version=latest” alt=”Documentation Status” /> </a> Tags Project has no tags. Short URLs lammps-helper.readthedocs.iolammps-helper.rtfd.io Default Version latest ‘latest’ Version master Read more here:…

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Issues installing Pindel from git

Issues installing Pindel from git 1 I’m currently attempting to install Pindel on my ubuntu machine (16.04 server), but have been having issues with running the ./INSTALL file. The ./INSTALL file takes the path to htslib as an argument, so I also installed htslib from git with git clone github.com/samtools/htslib

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Ensembl vep singularity

Ensembl vep singularity 0 Hello all, I would like to use variant effect prédictor on an hpc cluster. For that i use singularity with the docker image of vep : singularity pull –name vep.sif But i have a problem to use one plugin because a perl module is missing….

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lammps | Read the Docs

Repository github.com/aiidaplugins/aiida-lammps.git Project Slug aiida-lammps Last Built 3 months ago passed Maintainers Badge reStructuredText .. image:: readthedocs.org/projects/aiida-lammps/badge/?version=latest :target: aiida-lammps.readthedocs.io/en/latest/?badge=latest :alt: Documentation Status Markdown [![Documentation Status](https://readthedocs.org/projects/aiida-lammps/badge/?version=latest)](https://aiida-lammps.readthedocs.io/en/latest/?badge=latest) HTML <a href=”https://aiida-lammps.readthedocs.io/en/latest/?badge=latest”> <img src=”https://readthedocs.org/projects/aiida-lammps/badge/?version=latest” alt=”Documentation Status” /> </a> Tags Project has no tags. Short URLs aiida-lammps.readthedocs.ioaiida-lammps.rtfd.io Default Version latest ‘latest’ Version master Read more here:…

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Bacting | Zenodo

Zenodo DOI Badge DOI 10.5281/zenodo.5506884 Markdown [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5506884.svg)](https://doi.org/10.5281/zenodo.5506884) reStructedText .. image:: zenodo.org/badge/DOI/10.5281/zenodo.5506884.svg :target: doi.org/10.5281/zenodo.5506884 HTML <a href=”https://doi.org/10.5281/zenodo.5506884″><img src=”https://zenodo.org/badge/DOI/10.5281/zenodo.5506884.svg” alt=”DOI”></a> Image URL zenodo.org/badge/DOI/10.5281/zenodo.5506884.svg Target URL doi.org/10.5281/zenodo.5506884 Read more here: Source link

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Primer3 issue with the Sequence_ID

Primer3 issue with the Sequence_ID 0 Hi everyone, I am trying to sign primers for my sequences but I have an error that I do not understand the problem. I made my finputfile.txt and I made the command below: aka@aka:~/Desk/Primer$ /home/aka/primer3/src/primer3_core < input.txt > result.txt input.txt PRIMER_TASK=generic PRIMER_PICK_LEFT_PRIMER=1 PRIMER_PICK_INTERNAL_OLIGO=0 PRIMER_PICK_RIGHT_PRIMER=1…

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Gromacs: gmx_ffparams_t Struct Reference

#include <gromacs/topology/forcefieldparameters.h> Struct that holds all force field parameters for the simulated system. int  numTypes () const   Returns the number of function types, which matches the number of elements in iparams.   int  atnr = 0   The number of non-bonded atom types.   std::vector< t_functype >  functype  …

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Gromacs: src/gromacs/pbcutil/pbc.cpp File Reference

Implements routines in pbc.h. Utility functions for handling periodic boundary conditions. Mainly used in analysis tools. #define  BOX_MARGIN   1.0010   Margin factor for error message.   #define  BOX_MARGIN_CORRECT   1.0005   Margin correction if the box is too skewed.   enum   {   epbcdxRECTANGULAR = 1, epbcdxTRICLINIC, epbcdx2D_RECT, epbcdx2D_TRIC,   epbcdx1D_RECT, epbcdx1D_TRIC, epbcdxSCREW_RECT, epbcdxSCREW_TRIC,…

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How to load user-defined genome in IGV-webapp

How to load user-defined genome in IGV-webapp 0 I would like to create a session in IGV-webapp using a HTML file. The following works with pre-defined genomes (g.e. genome: “hg38”), but I would like to load my own genome. Is there a way to achieve this? <!DOCTYPE html> <html lang=”en”>…

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Error: NCBI C++ Exception – Invalid choice selection: NCBI-Seqalign::Score.value.real

Error: NCBI C++ Exception – Invalid choice selection: NCBI-Seqalign::Score.value.real 1 Hi, I am having issues running blast from command line, accessing remote databases. This is what i am running: blastn -db nt -query {input} -out {output} -evalue 0.001 -max_target_seqs 100 -remote Which returns this: Error: NCBI C++ Exception: T0 “/opt/conda/conda-bld/blast_1559335677723/work/c++/src/objects/seq/../seqalign/Score_.cpp”,…

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Gromacs: gmx::AnalysisDataStorageFrame Class Reference

#include <gromacs/analysisdata/datastorage.h> Allows assigning values for a data frame in AnalysisDataStorage. This class implements the necessary methods to add new data into the storage. AnalysisDataStorage::startFrame() returns an object of this type, which can be used to add one or more point sets to that data frame. When all data has…

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SCENIC-openloom not working

SCENIC-openloom not working 0 I have been trying to open a loom file which was produced by converting seurat object to loom.Using the following command: loom <- open_loom(loomPath) It is showing the following error : Error in H5File.open(filename, mode, file_create_pl, file_access_pl) : It is not possible to open the file….

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Gromacs: gmx::LegacyInput Class Reference

#include <gromacs/mdrun/simulatorbuilder.h> Collaboration diagram for gmx::LegacyInput: This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. [legend] Description Collection of legacy input information. Public Member Functions   LegacyInput (int filenamesSize, const t_filenm *filenamesData, t_inputrec *inputRec, t_forcerec *forceRec)   Build collection from legacy input data.  …

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Determining LOC coordinate from GFF3 start column

Determining LOC coordinate from GFF3 start column 0 Hi all, total noob question: I have a GFF3 file of a pepper (C. annuum) plant genome that looks like this: seqid src type start end chr01 PROTEIN gene 29119 37617 . – . ID=CA.PGAv.1.6.scaffold567.122 chr01 PROTEIN mRNA 29119 37617 . -…

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Endometriosis: gene identified which could be potential treatment target

Up to 10% of women experience endometriosis worldwide. The condition is chronic, extremely painful, and can result in infertility. Endometriosis happens when tissue similar to the lining of the uterus (the endometrium) grows outside of the uterus, in the abdominal cavity and sometimes on the ovaries and the fallopian tubes….

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Gromacs: gmx::Update Class Reference

#include <gromacs/mdlib/update.h> Description Contains data for update phase. Classes class   Impl   pImpled implementation for Update More…   Public Member Functions   Update (const t_inputrec *ir, BoxDeformation *boxDeformation)   Constructor.   gmx_stochd_t *  sd () const   Returns handle to stochd_t struct.   PaddedVector< gmx::RVec > *  xp ()…

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Install.sh · lammps

  # Install/unInstall package files in LAMMPS # mode = 0/1/2 for uninstall/install/update # this is default Install.sh for all packages # if package has an auxiliary library or a file with a dependency, # then package dir has its own customized Install.sh mode=$1 # arg1 = file, arg2 =…

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Gromacs: src/gromacs/listed-forces/disre.h File Reference

Declares functions for handling distance restraints. void  init_disres (FILE *fplog, const gmx_mtop_t *mtop, t_inputrec *ir, const t_commrec *cr, t_fcdata *fcd, t_state *state, gmx_bool bIsREMD)   Initiates *fcd data. More…   void  calc_disres_R_6 (const t_commrec *cr, int nfa, const t_iatom *fa, const rvec *x, const t_pbc *pbc, t_fcdata *fcd, history_t *hist)…

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bcl2fastq ERROR

bcl2fastq ERROR 1 Hi all, I have a problem. I’m running bcl2fastq software on Ubuntu, but I can’t demultiplex anything as the software gives me this error: *ERROR: bcl2fastq::common::Exception: 2021-Sep-02 12:12:34: Success (0): /home/Software/bcl2fastq/src/cxx/lib/layout/Layout.cpp(693): Throw in function void bcl2fastq::layout::handleDefaultSample(bool, bool, size_t, bcl2fastq::layout::LaneInfo&, bool&) Dynamic exception type: boost::exception_detail::clone_impl<bcl2fastq::common::InputDataError> std::exception::what: Missing a…

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CRISPR Applications in Medicine Depend on Minimizing Off-Target Editing

By Rolf Turk, PhD Genome editing technologies, such as CRISPR, are being applied to better understand basic biological systems as well as to research new kinds of gene and cell therapies. The CRISPR-Cas9 system comprises a Cas9 endonuclease protein that forms a complex with a guide RNA (gRNA) molecule, which…

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DeepMind releases a large database of 3D protein structures

WWith the advent of cheap gene sequencing, the world of biology is flooded with 2D data. Today, artificial intelligence is pushing the field up in three dimensions. On Thursday, Alphabet’s AI costume, DeepMind, used the precision deep learning model AlphaFold2 to capture the 3D structure of 350,000 proteins from the…

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Output per variant and per sample heterozygosity fraction from VCF.

Output per variant and per sample heterozygosity fraction from VCF. 2 As a QC measure I would like to know the per variant and per sample heterozygosity fraction. I already used vcftools to output the missingness per variant and sample. vcftools.github.io/man_latest.html Is there any tool that can do the same…

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install GenomicFeatures fail

install GenomicFeatures fail 1 @5b9023e7 Last seen 19 hours ago China BiocManager::install(‘GenomicFeatures’) results show ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: mirrors.tuna.tsinghua.edu.cn/CRAN/ Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.0 (2021-05-18) Installing package(s) ‘GenomicFeatures’ also installing the dependencies ‘Rhtslib’, ‘Rsamtools’, ‘GenomicAlignments’, ‘rtracklayer’ Packages which are only…

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Gromacs: src/gromacs/gmxlib Directory Reference

Directory dependency graph for gmxlib: This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. Files file   calcgrid.c   file   chargegroup.c   file   checkpoint.cpp   file   conformation-utilities.c   file   conformation-utilities.h   file   copyrite.cpp   file   disre.c   file…

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lammps – KSpace style for hybrid/overlay table and dipole?

I’m trying to run lammps for a system subject to a custom short-range potential, that I have in a table, as well as the lammps lj/cut/dipole/long interaction (with LJ epsilon set to 0 because I do not want its contribution) with ewald summation. I need to provide a kspace_style for…

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snsplot in Rshiny through images using reticulate

snsplot in Rshiny through images using reticulate 0 Hi, I’m using renderImage to show plots in a webpage based on the user input. But I see the plots are overlapping. output$dist_plot = renderImage({ db <- data() var = input$selected_gene data_gene <- as.numeric(data.frame(db[db$gene == var,-1])) sns$set_style(‘darkgrid’) sns$distplot(data_gene) plt$savefig(“https://www.biostars.org/p/9485849/Dist_plot.png”) list(src=”https://www.biostars.org/p/9485849/Dist_plot.png”) },deleteFile=FALSE) }…

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GROMACS: src/gromacs/ewald/pme_pp.h | Fossies

GROMACS: src/gromacs/ewald/pme_pp.h | Fossies “Fossies” – the Fresh Open Source Software Archive Member “gromacs-2021.3/src/gromacs/ewald/pme_pp.h” (18 Aug 2021, 5141 Bytes) of package /linux/privat/gromacs-2021.3.tar.gz: As a special service “Fossies” has tried to format the requested source page into HTML format using (guessed) C and C++ source code syntax highlighting (style: standard) with…

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GROMACS: src/gromacs/utility/any.h | Fossies

GROMACS: src/gromacs/utility/any.h | Fossies “Fossies” – the Fresh Open Source Software Archive Member “gromacs-2021.3/src/gromacs/utility/any.h” (18 Aug 2021, 8080 Bytes) of package /linux/privat/gromacs-2021.3.tar.gz: As a special service “Fossies” has tried to format the requested source page into HTML format using (guessed) C and C++ source code syntax highlighting (style: standard) with…

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Kaggle Lyft Motion Prediction for Autonomous Vehicles 4th place solution

Lyft Motion Prediction for Autonomous Vehicles Code for the 4th place solution of Lyft Motion Prediction for Autonomous Vehicles on Kaggle. Directory structure input — Please locate data here src |-ensemble — For 4. Ensemble scripts |-lib — Library codes |-modeling — For 1. training, 2. prediction and 3. evaluation…

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Pooling annotations from different databases in InterProScan

Pooling annotations from different databases in InterProScan 0 Is it acceptable to pool the annotations from the various sources InterProScan offers, and annotate a sequence with a subset of these? For example, if I have something like so: id annot src start stop seq1 dom1 Pfam 100 120 seq1 dom1a…

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