Tag: gitlab

A Standardized, Specification-Driven API Lifecycle

Transcript Lane: I’d like to share with you a high level view of why API specifications matter. How OpenAPI, AsyncAPI, JSON Schema and others are helping us standardize and deliver API lifecycle in a way that the machines understand. Also, allows us humans to better communicate, collaborate, and move forward…

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Porting GROMACS Across Heterogeneous Architectures

Porting GROMACS Across Heterogeneous Architectures In this second episode about GROMACS, one of the world’s most widely used open source molecular dynamics (MD) applications, we explore the quest to simplify portable, performant programming with Erik Lindahl, Biophysics Professor at Stockholm University & KTH Royal Institute of Technology, and Roland Schulz,…

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Predicting the structure of large protein complexes using AlphaFold and sequential assembly

Abstract AlphaFold and AlphaFold-multimer can predict the structure of single- and multiple chain proteins with very high accuracy. However, predicting protein complexes with more than a handful of chains is still unfeasible, as the accuracy rapidly decreases with the number of chains and the protein size is limited by the…

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Senior Bioinformatics Engineer, remote in Marlborough, MA at Quest Diagnostics

Look for more than answers. At Quest, we are on a continuous journey of discovery and development. It’s this attitude that has made us an industry leader and the #1 Diagnostic Lab in the US. For those joining us, we offer exciting and fast-moving career opportunities where you can affect…

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LIMS Developer, Bioinformatics, remote at Quest Diagnostics

Look for more than answers. At Quest, we are on a continuous journey of discovery and development. It’s this attitude that has made us an industry leader and the #1 Diagnostic Lab in the US. For those joining us, we offer exciting and fast moving career opportunities where you can…

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Petabase-scale sequence alignment catalyses viral discovery

Serratus alignment architecture Serratus (v0.3.0) (github.com/ababaian/serratus) is an open-source cloud-infrastructure designed for ultra-high-throughput sequence alignment against a query sequence or pangenome (Extended Data Fig. 1). Serratus compute costs are dependent on search parameters (expanded discussion available: github.com/ababaian/serratus/wiki/pangenome_design). The nucleotide vertebrate viral pangenome search (bowtie2, database size: 79.8 MB) reached processing rates…

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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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Moodle Authentication for JupyterHub Docker image | Moodle | Docker | Python | GitLab | OAuth

I have a JupyterHub installation managed within Docker. Also, I have a Moodle installation. I need a freelancer who is competent in both JupyterHub configuration and Moodle configuration. The task is to take my GitLab repository of the JupyterHub Docker file as a basis, create a new branch and do…

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Your Code-First API Needs Validation

[*] When you start a project, you might tend to do code first API as this is a well-known territory for most developers, especially with frameworks like Spring Boot, which uses powerful annotations to generate your API and specifications. In a matter of a few lines, you have a simple…

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4 Use Cases of OpenAPI Which Are Good to Know | by Na’aman Hirschfeld | Dec, 2021

An introduction to OpenAPI with use cases Photo by Gertrūda Valasevičiūtė on Unsplash In this article I offer an introduction to OpenAPI (OA) and some of its more interesting use cases. If you are already familiar with what OA is, you can skip ahead to the use-cases part of this…

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Accepted golang-github-go-openapi-jsonpointer 1:0.19.5-3 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Tue, 30 Nov 2021 15:26:00 +0100 Source: golang-github-go-openapi-jsonpointer Architecture: source Version: 1:0.19.5-3 Distribution: unstable Urgency: medium Maintainer: Debian Go Packaging Team <team+pkg…@tracker.debian.org> Changed-By: Guillem Jover <gjo…@sipwise.com> Changes: golang-github-go-openapi-jsonpointer (1:0.19.5-3) unstable; urgency=medium . * Team upload. * Add Repository and Repository-Browse fields…

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How we got to OpenAPI

November 23, 2021 A story about how we went from spontaneous api code writing to a process with a separate repository of api schemas and code generation based on them. TL;DR We were living with an unstructured websocket API of our own design, but realized that it was impossible to…

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QIAGEN hiring Bioinformatics Scientist in United States

Overview At the heart of QIAGEN’s business is a vision to make improvements in life possible. We are on an exciting mission to make a real difference in science and healthcare. We are still the entrepreneurial company we started out as and have today achieved a size where we can…

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Developer – Java at Parvana Recruitment

Responsibilities: Developing green field microservices to run in a cloud native environment using Java. Developing high quality code using the best tools and practices. Designing, coding, testing, debugging, documenting and maintaining microservice applications and application enhancements. Supporting CI/CD tools integration. Collaborating with other team members on application architecture design and…

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Bioinformatics scientist (Full-time/Permanent) for the analysis of multiomics data in oncology

Position of Bioinformatics scientist (Full-time/Permanent) for the analysis of multiomics data in oncology, at Evotec Toulouse (France) to be filled as soon as possible. www.evotec.com/en General Summary : For our site in Toulouse, France, we have an exciting opportunity for a dedicated and professional Bioinformatics Scientist – Full time and…

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Bioinformatics DevOps Engineer, remote at Quest Diagnostics in Alameda, California

Job Description: Look for more than answers. At Quest, we are on a continuous journey of discovery and development. It’s this attitude that has made us an industry leader and the #1 Diagnostic Lab in the US. For those joining us, we offer exciting and fast moving career opportunities where…

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gromacs 2021.4 – Download, Browsing & More

gromacs 2021.4 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of gromacs-2021.4.tar.gz (5 Nov 09:47, 38023262 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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Research Engineer (RE123)

Job:Research Engineer (RE123) 0 Context And Mission Professor Nataša Pržulj is looking for a Research Support Engineer to work in her Integrative Computational Network Biology (ICONBI) group (overview of the group is at www.bsc.es/discover-bsc/organisation/scientific-structure/integrative-computational-network-biology-iconbi).The post-holder will participate in the process of finding, designing and implementing new algorithms, Data Science and…

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Advanced Bioinformatics Data Scientist job at BenevolentAI, November 2021

With over 35 nationalities and a range of backgrounds represented in our Benevolent team, we aim to build an inclusive environment where our people can bring their authentic selves to work, be respected for who they are and the exceptional work they do. We welcome and actively encourage applications from…

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SR. Bioinformatics Software Engineer – CMO

Job:SR. Bioinformatics Software Engineer – CMO – MSKCC 0 Senior Bioinformatics Engineer Company Overview At Memorial Sloan Kettering (MSK), we’re not only changing the way we treat cancer, but also the way the world thinks about it. By working together and pushing forward with innovation and discovery, we’re driving excellence…

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NGSeq/DHPGIndex: This tool is for compressing and indexing pan-genomes and genome sequence collections for scalable sequence and read alignment purposes.

General This tool is for compressing and indexing pan-genomes and genome sequence collections for scalable sequence and read alignment purposes. The pipeline can be deployed in cloud computing environment or in dedicated computing cluster. The tool extends the CHIC aligner gitlab.com/dvalenzu/CHIC with distributed and scalable features. DHPGIndex have been tested…

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The genome of Shorea leprosula (Dipterocarpaceae) highlights the ecological relevance of drought in aseasonal tropical rainforests

Sequencing of Shorea leprosula genome Sample collection Leaf samples of S. leprosula were obtained from a reproductively mature (diameter at breast height, 50 cm) diploid tree B1_19 (DNA ID 214) grown in the Dipterocarp Arboretum, Forest Research Institute Malaysia (FRIM). DNA extraction Genomic DNA was extracted from leaf samples using the…

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How To Extract A Sequence From A Big (6Gb) Multifasta File ?

How To Extract A Sequence From A Big (6Gb) Multifasta File ? 11 I want to extract some sequences using ID from a multifasta file. Using perl is not possible because it gave an error when indexing the database. Maybe because of it’s size? Is there any way to this…

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Postdoctoral Fellow – Translational Research in Diabetes – Bioinformatics and Computational Science

Job Description About City of Hope City of Hope, an innovative biomedical research, treatment and educational institution with over 6,000 employees, is dedicated to the prevention and cure of cancer, type 1 diabetes, type 2 diabetes and other life-threatening diseases and guided by a compassionate, patient-centered philosophy. City of Hope…

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Postdoctoral Fellow – Translational Research in Diabetes – Bioinformatics and Computational Science job with City of Hope

About City of Hope City of Hope, an innovative biomedical research, treatment and educational institution with over 6,000 employees, is dedicated to the prevention and cure of cancer, type 1 diabetes, type 2 diabetes and other life-threatening diseases and guided by a compassionate, patient-centered philosophy. City of Hope has one…

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biopython extract sequence from fasta

My two questions are: What is the simplest way to do this? This unique book shows you how to program with Python, using code examples taken directly from bioinformatics. using python-bloom-filter, just replace the set with seen = BloomFilter(max_elements=10000, error_rate=0.001). This book is suitable for use as a classroom textbook,…

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Full Stack DevOps Software Developer Jobs in Grenoble (38) at European Molecular Biology Laboratory –

EMBL Grenoble is looking for a Full-Stack Software Developer to join the Crystallographic Information Management System (CRIMS) project. The Marquez Team operates the High Throughput Crystallization Laboratory (HTX Lab), one of the largest facilities of its kind in Europe and has developed automated pipelines for macromolecular crystallography and fragment screening…

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Web Developer at European Molecular Biology Laboratory (EMBL)

About the team/job IT Services operates and supports the IT infrastructure and services at EMBL headquarters in Heidelberg and at the laboratory’s sites in Barcelona and Rome. In collaboration with the EMBL-EBI in Cambridge our team is creating and implementing a new web infrastructure for all EMBL websites. We are…

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Where can I get ?or how can I make a mappability track for hg38 assembly

Where can I get ?or how can I make a mappability track for hg38 assembly 2 Lucky you @manojmumar_bhosale I worked on similar problem recently and therefore have the bash script you can use. Required tools: GEM libary from here UCSC’s wigToBigWig from here (I chose binary for Linux 64…

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Setup my Github repo in a Kaggle environment | Python

I would like step by step instructions to: 1. Set up Git so that commands like “git pull” work within the provided linux environment 2. Create a Conda environment (or overwrite the existing one) in this Kaggle environment, generated from my own [login to view URL] file 3. Preserve all…

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Bioinformatics Software Engineer, Cancer Genomics Research Laboratory (req2036) job with Frederick National Laboratory

PROGRAM DESCRIPTION We are seeking an enthusiastic, creative, and collaborative bioinformatics software engineer to support pipeline development and analysis for our broad portfolio of genomic studies. If you have experience designing and deploying robust, reproducible, production-quality pipelines, then come join our talented team of bioinformaticians dedicated to understanding the genetics…

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