Tag: Java

Scatter Gather principle by chromosome on Gatk

Scatter Gather principle by chromosome on Gatk 0 Hi all, On a quest to optimize gatk pipeline, I met scatter gather principle, so I did following, pids= for chr in chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20…

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How to autogenerate test cases from openapi v3 description using spring boot/java

I want to create a tool that will accept the “OpenAPI v3 definition” document as input. Based on that, it will generate basic test cases to validate/check the API behaviour using Java/Spring Boot. Can someone please help with that or give me some suggestions on how I can achieve this?…

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VIB hiring Postdoc Position in Bioinformatics, Metagenomics and the Human Microbiome in Leuven, Flemish Region, Belgium

The lab of Jeroen Raes (VIB, KU Leuven) is looking for a postdoctoral researcher in the computational analysis of microbiome data, with a particular emphasis on human-associated microbial communities in health and disease.Projects Will Focus On(i) bioinformatics/statistics method development for joint host and microbiota data analysis, multi-omics and clinical data…

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Research Fellow – Bioinformatics Program Job

Key Skills Java Programming, Python Programming, C++, C Programming, SQL, Cloud computing, Scala Programming, Machine learning techniques, Data science techniques, MATLAB Programming, PyTorch, TensorFlow, R Programming Job Description The Research shield at Mayo Clinic is committed to creating a diverse environment and recognizes that diverse research teams make better decisions,…

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Bioinformatics Analyst II Job in Maryland (MD), Research and Development Career, Full Time Jobs in Frederick National Laboratory for Cancer Research

Bioinformatics Analyst II Job ID: req3154Employee Type: exempt full-timeDivision: Applied & Development Research ProgramFacility: Frederick: Ft DetrickLocation: PO Box B, Frederick, MD 21702 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical…

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Senior Research Scientist, Bioinformatician Cancer Science Institute job with NATIONAL UNIVERSITY OF SINGAPORE

Job Description A Senior Research Scientist position is available immediately in Prof Chng Wee Joo’s groups for a highly motivated PhD graduate with experience in Bioinformatics (computational genomics). The focus of the lab is on deciphering transcriptional and genomic abnormalities in the context of blood cancer, including epigenetic and superenhancer deregulation, using single…

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Bioinformatics Analyst III Position In South San Francisco, CA

Job Description To discuss more about this job opportunity, please reach out to Chitrank Rastogi (LinkedIn URL – www.linkedin.com/in/chitrank-rastogi-55119a102/), email your updated resume at chitrank.rastogi@collabera.com or give me a call at (425) 523-1648. Thank you! Job Description:Job Roles & Responsibilities: The Genomic Research Center Computational Oncology group (GRC-CO) is seeking…

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Intern- Bioinformatics (PHD) (NE) – AI&I at Mayo Clinic

Why Mayo ClinicMayo Clinic is the nation’s best hospital (U.S. News & World Report, 2022-2023) and ranked #1 in more specialties than any other care provider. We have a vast array of opportunities ranging from Nursing, Clinical, to Finance, IT, Administrative, Research and Support Services to name a few. Across…

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ImageJ measuring plot areas causes crash: java.lang.ArrayIndexOutOfBoundsException: 200

ImageJ measuring plot areas causes crash: java.lang.ArrayIndexOutOfBoundsException: 200 0 I’m measuring the areas under curves from gel lane plots in Fiji (i.e. ImageJ 1.53t with Java 1.8.0_322) by drawing lines on the plots and then using the magic wand tool to select the area, which returns a value. After doing…

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java – I am unable to execute the fastqc command in HPC cluster

I am trying to run fastqc for fastq.gz files in RNA-seq Data analysis and I have written a PBS script. However, I am encountering the following error Can’t exec “java”: No such file or directory at /home/paksls/Atreya/software/FastQC/fastqc line 307 I have written the following script: #!/bin/bash #PBS -l nodes=1:ppn=6,pmem=10240MB,walltime=04:00:00 #PBS…

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Senior Clinical Bioinformatics Scientist – Medical Center, New York, United States

Senior Clinical Bioinformatics Scientist 525626 Medical Center Institute for Genomic Medicine Full Time Grade 104 Job Type: Officer of Administration Bargaining Unit: Regular/Temporary: Regular End Date if Temporary: Hours Per Week: 35 Salary Range:   Position Summary The Precision Genomics Laboratory (PGL), a partnership between the Department of Pathology and…

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java – openapi-generator not generating model

I am using the openapi-generator to create a multipart/form-data. In an ideal situation I should be able to upload a file, and specify in the options what should happen with the file. I would like the options to be an object. For one or another reason, this does not seem…

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Senior Development Lead – Java OpenAPI RESTful API – Page Group Hong Kong

Leadership role:- You will be responsible for supporting the system design and conducting the development to deliver the business solution for the project according to the requirements and engineering standards. He/she will perform system analysis, application development, unit testing, trouble-shooting, and operations support work. Client Details We are an forward…

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Unsure how to run FastQC on interactive node : bioinformatics

Hi all. My goal has long been to get involved in biology-problems — especially in the biomedical realm, but I haven’t had a direct path to doing so because I don’t love “doing” biology itself. For instance, I did a BS and MS in applied math with a healthy dose…

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Staff Scientist Bioinformatics – Thermo Fisher Scientific

Job Profile: Staff Scientist, Bioinformatics Location: South San Francisco, California, US Job ID: 205404BR Date Posted: 19 Sept. 2022 Job Overview When you’re part of the team at Thermo Fisher Scientific, you’ll do important work, like helping customers in finding cures for cancer, protecting the environment or making sure our…

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Research Fellow, Bioinformatician – Cancer Science Institute job with NATIONAL UNIVERSITY OF SINGAPORE

Job Description A postdoctoral position is available immediately in Prof Chng Wee Joo’s groups for a highly motivated PhD graduate with experience in Bioinformatics (computational genomics). The focus of the lab is on deciphering transcriptional and genomic abnormalities in the context of blood cancer, including epigenetic and superenhancer deregulation, using single cell…

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Bioinformatics Scientist I/II – Codexis

          Are you ready to join our mission to improve the health of people and the planet?  Do you have a passion for science and the transformational role that enzymes are playing?   Come be part of our team at Codexis, Inc. We are a leading enzyme engineering company leveraging our…

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Index of /~birch/birchhomedir/java/Mesquite_Folder/mesquite/trees/BasicTreeWindowMaker/recent

Name Last modified Size Description Parent Directory   –   recent0.gif 2003-09-04 01:59 915   recent1.gif 2003-09-04 01:58 922   recent2.gif 2003-09-04 01:59 925   recent3.gif 2003-09-04 01:59 932   recent4.gif 2003-09-04 02:00 936   recent5.gif 2003-09-04 01:57 935   recent6.gif 2003-09-04 01:57 940   recent7.gif 2003-09-04 01:57 940  …

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Principal Software Engineer – Bioinformatics Job in Mississauga, Ontario – Hoffmann-La Roche Ltd

Impact HealthcareRoche Sequencing is not only changing science, but we are changing lives. Our software teams are laying the groundwork for the future by developing powerful bioinformatics algorithms, data analysis tools, and software/systems infrastructures so researchers and clinicians can make better health decisions faster. The path to curing cancer lies…

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How to Choose the Right Bioinformatics Position in 2022?

When you’re looking to land a good bioinformatics job, whether you’re a fresher, a career changer, or an experienced candidate, there’s usually a lot on your mind. And although the job search phase can look intimidating and exhausting, there has never been a better time to start a career in…

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Data Management Coordinator – Germany Jobs IT Engineering Academic Remote NGO Charity Work

About the team/jobThe Data Science Centre, launched in February 2022 to promote cutting-edge research and services in Data Science across all of EMBL, is looking for a bioinformatician, computational biologist or computer scientist as a Data Management Coordinator. The Data Science Centre will ensure that biological research data at our…

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Swagger: Specify Two Responses with the Same Response Code

1. Overview In this article, we’ll write an API specification that allows returning two different objects for the same response code. We’ll demonstrate how we can use that specification to generate Java code and the Swagger documentation. 2. Presentation of the Problem Let’s define two objects. A Car has an…

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Struts Problem Report

Struts Problem Report Struts Problem Report Struts has detected an unhandled exception: Messages: actions.Fusions.fusion?geneNameA=ZBTB1&geneNameB=MTHFD1() File: java/lang/Class.java Line number: 1,786 Stacktraces java.lang.NoSuchMethodException: actions.Fusions.fusion?geneNameA=ZBTB1&geneNameB=MTHFD1() java.lang.Class.getMethod(Class.java:1786) org.apache.struts2.interceptor.validation.AnnotationValidationInterceptor.getActionMethod(AnnotationValidationInterceptor.java:75) org.apache.struts2.interceptor.validation.AnnotationValidationInterceptor.doIntercept(AnnotationValidationInterceptor.java:47) com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:98) com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:242) com.opensymphony.xwork2.interceptor.ConversionErrorInterceptor.intercept(ConversionErrorInterceptor.java:138) com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:242) com.opensymphony.xwork2.interceptor.ParametersInterceptor.doIntercept(ParametersInterceptor.java:238) com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:98) com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:242) com.opensymphony.xwork2.interceptor.ParametersInterceptor.doIntercept(ParametersInterceptor.java:238) com.opensymphony.xwork2.interceptor.MethodFilterInterceptor.intercept(MethodFilterInterceptor.java:98) com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:242) com.opensymphony.xwork2.interceptor.StaticParametersInterceptor.intercept(StaticParametersInterceptor.java:191) com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:242) org.apache.struts2.interceptor.MultiselectInterceptor.intercept(MultiselectInterceptor.java:75) com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:242) org.apache.struts2.interceptor.CheckboxInterceptor.intercept(CheckboxInterceptor.java:90) com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:242) org.apache.struts2.interceptor.FileUploadInterceptor.intercept(FileUploadInterceptor.java:252) com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:242) com.opensymphony.xwork2.interceptor.ModelDrivenInterceptor.intercept(ModelDrivenInterceptor.java:100) com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:242) com.opensymphony.xwork2.interceptor.ScopedModelDrivenInterceptor.intercept(ScopedModelDrivenInterceptor.java:141) com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:242) com.opensymphony.xwork2.interceptor.ChainingInterceptor.intercept(ChainingInterceptor.java:145) com.opensymphony.xwork2.DefaultActionInvocation.invoke(DefaultActionInvocation.java:242) com.opensymphony.xwork2.interceptor.PrepareInterceptor.doIntercept(PrepareInterceptor.java:171)…

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a new and efficient development model, to achieve code and API separation, efficient development, development must see!!!

什么是openapi 3.0 OpenAPI 3.0.0 是 OpenAPI The first official version of the specification,因为它是由 SmartBear Software 捐赠给 OpenAPI Initiative,并在2015年从 Swagger 规范重命名为 OpenAPI 规范. 介绍: OpenAPI 规范(OAS),is to define a standard、programming language-independentRESTful API的规范.OpenAPI Specifications enable both humans and computers to“Do not contact with any program source code and documentation、Does not monitor network…

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Index of /~psgendb/birchhomedir/public_html/doc/pkg/samtools-1.7/misc

Name Last modified Size Description Parent Directory   –   HmmGlocal.java 2014-08-01 09:48 9.0K   ace2sam.c 2016-05-10 08:11 11K   blast2sam.pl 2017-09-14 10:20 5.2K   bowtie2sam.pl 2014-08-18 14:29 3.3K   export2sam.pl 2014-08-01 09:48 18K   interpolate_sam.pl 2014-08-18 14:29 6.0K   maq2sam.c 2017-12-12 11:10 7.2K   md5fa.c 2017-07-24 09:15 2.8K  …

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Bioinformatics Analyst I/II in Seattle, WA for Fred Hutchinson Cancer Research Center

Details Posted: 13-Aug-22 Location: Seattle, Washington Type: Full-time Salary: Open Overview Fred Hutchinson Cancer Center is an independent, nonprofit, unified adult cancer care and research center that is clinically integrated with UW Medicine, a world leader in clinical care, research and learning. The first National Cancer Institute-designated cancer center in…

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Bioinformatics Analyst at MedGenome Labs

Job Purpose Understand complex research problems and design and implement bioinformatics solutions working with the team members. Job Responsibilities:Understand complex research problems and design and implement bioinformatics solutions working with the team members Support impactful data analysis of high-throughput data generated for clinical diagnosis Understand industry standard pipelines, algorithms and…

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OpenAPI: combine JAXB and JSON (WRAPPER_OBJECT) correctly?

OpenAPI: combine JAXB and JSON (WRAPPER_OBJECT) correctly? Dear community, I’m a beginner with swagger/openapi. I want write Java classes with annotations and generate documentation by OpenAPI library. In my gradle project I use: implementation “io.swagger.core.v3:swagger-core:2.2.2” implementation ‘io.swagger.core.v3:swagger-annotations:2.2.2’ implementation “io.swagger.core.v3:swagger-jaxrs2:2.2.2” implementation ‘com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:2.13.2’ implementation ‘com.fasterxml.jackson.datatype:jackson-datatype-jdk8:2.13.2’ implementation ‘com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.13.2’ My demo class is: @XmlRootElement(name…

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Research Bioinformatician II – Li Lab – Computational Biomedicine

Everyone’s unique health journey is informed by data. Join us as we translate today’s discoveries into tomorrow’s medicine! Cedars-Sinai is home to some of the most advanced biomedical research and training programs in the world, which attracts renowned physician-scientists seeking an unparalleled environment for fostering invention and teamwork. The Department…

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Bioinformatic jobs in Marina South City Park – July 2022

Bayes–Central Singapore The ideal candidate will have an established track record in the field of structural biology, molecular dynamics and possess a broad base… National Cancer Centre Singapore–Outram We are recruiting Bioinformatics Specialists and Postdoctoral Fellows at the Cancer Discovery Hub, National Cancer Centre Singapore. You… $1,000 – $1,000 per…

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Senior Bioinformatics Scientist at Roche July, 2022

Position summary As a Senior Bioinformatics Scientist, you will provide bioinformatics support for product research and development, as well as the marketing, sales and on-market product support teams. You will collaborate and innovate with bioinformatics scientists, software engineers and  molecular biologists to build products that will impact patient care for…

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Standalone GATK HaplotypeCaller : bioinformatics

Hello! I’m hoping someone can direct me to resources around acquiring or building standalone gatk tools, specifically HaplotypeCaller. All of my research has led to the monolithic gatk wrapper (either local, spark, or in docker). The big tool is brilliant and I’ve been using it thus far, but it’s pretty…

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NHLS Vacancies for Nurses – Bioinformatics Scientist

vacancieshutem 2 mins ago Job Responsibilities: Engage with NICD users and assist with next-generation sequencing (NGS) data analysis .Perform basic and advanced analysis and interpretation on data produced from next generation sequencing systems (e.g. Illumina, PacBio or Ion torrent platforms) as well as…

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A*STAR Research hiring #SGUnitedJobs Bioinformatics Specialist, Laboratory of Systems Biology & Data Analytics, GIS in Singapore, Singapore

The Genome Institute of Singapore (GIS) is an institute of the Agency for Science, Technology and Research (A*STAR). It has a global vision that seeks to use genomic sciences to achieve extraordinary improvements in human health and public prosperity. GIS is dedicated to creating a social culture that is focused…

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Open Rank Bioinformatics Software Engineer I and Bioinformatics Engineer II in Baltimore, MD for University of Maryland, Baltimore

Open Rank Bioinformatics Software Engineer I and Bioinformatics Software Engineer II The Institute for Genome Sciences (IGS), Informatics Resource Center, is recruiting for a Open Rank Bioinformatics Software Engineer I and Bioinformatics Software Engineer II position. This position will be filled as either the Bioinformatics Software Engineer I or II.IGS…

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Three families of Asgard archaeal viruses identified in metagenome-assembled genomes

Liu, Y. et al. Expanded diversity of Asgard archaea and their relationships with eukaryotes. Nature 593, 553–557 (2021). CAS  PubMed  Google Scholar  Dombrowski, N., Teske, A. P. & Baker, B. J. Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments. Nat. Commun. 9, 4999 (2018). PubMed  PubMed…

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Senior Software Developer (commencing immediately) at European Molecular Biology Laboratory (EMBL)

Contract Type: Staff Member Location: EMBL-EBI, Hinxton near Cambridge, UK Job Function: Senior Technical Officer (gr. 6-8) Contract Duration-Length of Time (years/months): 1 year (until grant-end date of 30/10/2023) Contract Duration-Is this renewable to 9 years?: No Advertised Grade-Grading: Grade 6 (monthly salary starting at £3,143.06 after tax plus benefits) About the team/job We are seeking…

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BAM – Job openings – Data Scientist for additive manufactruing (m/f/d) in the field of business informatics, computer science, software development, bioinformatics, engineering, data management, physics, data engineering or comparable

Section S.3 – eScience To strengthen our team in the division “eScience” in Berlin-Steglitz, starting as soon as possible, we are looking for a Data Scientist for additive manufactruing (m/f/d) in the field of business informatics, computer science, software development, bioinformatics, engineering, data management, physics, data engineering or comparable Salary…

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St. Jude Children’s Research Hospital hiring Bioinformatics Analyst in Memphis, Tennessee, United States

The Chi Lab is seeking a Systems Immunology Specialist to work on exciting projects related to immune signaling and metabolism in the St. Jude Deparment of Immunology. One of the premier pediatric research institutions in the world, St. Jude Children’s Research Hospital provides exceptional resources, a collaborative environment, and access to…

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Bioinformatics Analyst at Dana-Farber Cancer Institute in 450 Brookline Ave, Boston, MA

Located in Boston and the surrounding communities, Dana-Farber Cancer Institute is a leader in life changing breakthroughs in cancer research and patient care. We are united in our mission of conquering cancer, HIV/AIDS and related diseases. We strive to create an inclusive, diverse, and equitable environment where we provide compassionate…

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Postdoctoral position in bioinformatics of Evo-Devo

Vous voyez une version de l’annonce optimisée pour les appareils mobiles. Annonce originale Introduction UNIL is a leading international teaching and research institution, with over 5,000 employees and 17,000 students split between its Dorigny campus, CHUV and Epalinges. As an employer, UNIL encourages excellence, individual recognition and responsibility. Presentation The…

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python 3.x – PySpark on Jupyterhub K8s || Unable to query data || Class org.apache.hadoop.fs.s3a.S3AFileSystem not found

Pyspark Version: 2.4.5 Hive Version: 1.2 Hadoop Version: 2.7 AWS-SDK Jar: 1.7.4 Hadoop-AWS: 2.7.3 When I am trying to show data I am getting Class org.apache.hadoop.fs.s3a.S3AFileSystem not found while I am passing all the information which all are required. I passed all three for this config fs.s3.aws.credentials.provider org.apache.hadoop.fs.s3a.BasicAWSCredentialsProvider com.amazonaws.auth.InstanceProfileCredentialsProvider com.amazonaws.auth.EnvironmentVariableCredentialsProvider…

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linux merge multiple files in picard

Why not use samtools? for folder in my_bam_folders/*; do samtools merge $folder.bam $folder/*.bam done In general, samtools merge can merge all the bam files in a given directory like this: samtools merge merged.bam *.bam EDIT: If samtools isn’t an option and you have to use Picard, what about something like…

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Bioinformatics Specialist I — Cancer Computational Biology —- Cancer Center in Boston, MA for MGH Institute of Health Professions

Details Posted: 05-Jun-22 Location: Boston, Massachusetts Salary: Unpaid Internal Number: 3190190-3499_1654275737 URLs: www.massgeneral.org/cancer-center/clinical-trials-and-research/center-for-cancer-research/investigators/rheinbay-lab www.massgeneral.org/cancer-center/clinical-trials-and-research/center-for-cancer-research/investigators/lawrence-lab Unique opportunity to join an interdisciplinary team bridging the Harvard Medical School, the Massachusetts General Hospital, and the Broad Institute of Harvard and MIT. The Rheinbay Lab and Lawrence Lab at the Massachusetts General Hospital Cancer…

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BBMap 38.90-GCC-10.2.0 (for BlueBEAR, BEARCloud VMs, and CaStLeS VMs)

BBMap 38.90-GCC-10.2.0 Unsupported: Use of this version of BBMap is not supported. More information on our Applications Support and Retention Policy. BBMap short read aligner, and other bioinformatic tools. Accessing BBMap 38.90-GCC-10.2.0 To load the module for BBMap 38.90-GCC-10.2.0 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs,…

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Index of /~psgendb/birchhomedir/admin/launchers/biolegato.app/Contents/Resources/local/java/TIGR/MeV_4_6_1/R-2.9.1/library/spatial/html

Name Last modified Size Description Parent Directory   –   00Index.html 2010-11-01 11:48 3.8K   Kaver.html 2010-11-01 11:48 1.9K   Kenvl.html 2010-11-01 11:48 2.2K   Kfn.html 2010-11-01 11:48 2.4K   Psim.html 2010-11-01 11:48 1.7K   SSI.html 2010-11-01 11:48 1.9K   Strauss.html 2010-11-01 11:48 2.1K   anova.trls.html 2010-11-01 11:48 1.9K  …

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Bioinformatics Remote Jobs – Find popular part time/ full time remote Bioinformatics jobs

Explore 2 recent remote Bioinformatics jobs & apply for free. Biology Breed new fish for sportfishing Hourly – Posted at 5 hours ago $19.43Hourly Jun 20, 2022Expiry We need help creating a new species of fish to the Sportfishing industries. The fish is to be stocked & produced by a…

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Index of /~psgendb/doc/local/java/MAExplorer/lib/MAERlibr/man

Name Last modified Size Description Parent Directory   –   mae.colorBased3dPlot..> 2005-02-19 16:02 1.2K   mae.colorBasedMatrix..> 2005-02-19 16:02 1.1K   mae.getCondHData.Rd 2005-02-19 16:02 897   mae.getCondVData.Rd 2005-02-19 16:02 889   mae.getVSfromHScondD..> 2005-02-19 16:02 1.6K   mae.loessPlot.Rd 2005-02-19 16:02 1.2K   mae.maXYpvalue.Rd 2005-02-19 16:02 898   mae.readHSfile.Rd 2005-02-19 16:02 1.5K  …

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Detailed differences between sambamba and samtools

3 month , My first post in the new student group , The false-positive mutation appears because duplicates mark Not enough ?, Tells the story of supplementary read It won’t be GATK MarkDuplicates Marked as duplicates The problem of . after , In response to this question , I began…

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Bioinformatics Scientist at Abterra Biosciences

Benefits pulled from the full job description Dental insurance health insurance on-site gym retirement plan Responsibilities: Develop and implement novel algorithms to support our antibody discovery, sequencing, and repertoire analysis.Work closely with molecular biologists and protein chemists to improve existing and develop novel methods.Perform analysis of internal, public, and collaborator…

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java – Calculating physico-chemical properties of amino acids in Biojava

I need to calculate the number and percentages of polar/non-polar, aliphatic/aromatic/heterocyclic amino acids in this protein sequence that I got from UNIPROT, using BioJava. I have found in the BioJava tutorial how to read the Fasta files and implemented this code. But I have no ideas how to solve this…

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A*STAR – Agency for Science, Technology and Research hiring Bioinformatics Specialis, Laboratory of Systems Biology & Data Analytics, GIS in Singapore, Singapore

 The Genome Institute of Singapore (GIS) is an institute of the Agency for Science, Technology and Research (A*STAR). It has a global vision that seeks to use genomic sciences to achieve extraordinary improvements in human health and public prosperity. GIS is dedicated to creating a social culture that is…

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Recent questions tagged fasta – Q&A

Most popular tags python javascript html java css reactjs c# php r sql arrays pandas c++ android jquery DataFrame python-3.x node.js c mysql list flutter JSON ios typescript sql-server swift string angular regex laravel excel django dictionary dart bash numpy postgresql loops oracle vba linux angularjs function for-loop spring spring-boot…

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OpenApi 3.0.3 code gen for Java Backend question

I have recently started to look at OpenApi code generator and I have a few questions that I couldn’t find an answer to with the usual resources (google and documentation mostly). What I want to generate via the components.yaml and the code generator: An interface with a couple of methods…

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Research Associate II, Bioinformatics at Sherlock Biosciences

Job details Salary $65,546 – $106,525 a year job type full-time Full job description Job description:Summary/objective: As part of this role, you will support the bioinformatics team in building a comprehensive bioinformatics software that informs the design of next generation molecular diagnosticsTogether with your mentor, you will refine and expand…

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Running fastqc

Running fastqc 1 I am trying to run fastqc from my home directory using the command line. I do not have access to the root directory. I have downloaded fastqc zip file and unzipped it. When going into the FastQC directory, the following options are available: Configuration, LICENSE_JHDF5.txt, cisd-jhdf5.jar, net…

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Mbedtls Application On Tcp

How to use mbedTLS library in Keil or IAR IDEs? I want to do an RSA encryption/decryption using my AT91SAM7S256 ARM MCU.After googling I found mbed TLS library. The IP networking interface includes TLSSockets which behave similarly to normal TCP sockets but automatically use Mbed TLS to set up a…

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Roche hiring Principal Bioinformatics Software Engineer, Java Development in Santa Clara, California, United States

This position may be based out of Santa Clara, California, USA, with remote work locations possible in The United States.Impact HealthcareRoche Sequencing is not only changing science, but we are changing lives. Our software teams are laying the groundwork for the future by developing powerful bioinformatics algorithms, data analysis tools,…

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Principal Bioinformatics Scientist I (REMOTE) job with F. Hoffmann-La Roche AG

Job Description We are seeking a committed and driven Principal Bioinformatics Scientist for our Computational Bioinformatics Research and Early Development team. We have a team of skilled bioinformatics researchers working in a highly collaborative environment with multiple internal and external teams. The work will be focused on developing novel methods…

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Manager of Bioinformatics in Chicago, IL for University of Chicago (UC)

Details Posted: 22-Apr-22 Location: Chicago, Illinois Type: Full-time Salary: Open Categories: Research – Laboratory/Non-Laboratory Staff/Administrative Location: Hyde Park Campus Job Description: Leads a team of bioinformaticians and provides technical guidance for the team to follow best practices and deliver data production timely. Collaborates cross-functionally with our user services, software engineering,…

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can`t find a path for to file

Trimmomatic – can`t find a path for to file 1 I simply need to run Trimmomatic, but he doesn`t see input files. May be you know how to deal with it? #creating variables INPUT_DIR=”path/folderinput” OUTPUT_DIR=”path/folderoutput” APPENDIX=”.fastq.gz” APPENDIX1=”_R1.fastq.gz” APPENDIX2=”_R2.fastq.gz” TRIMMOMATIC=”java -jar /home/path/trimmomatic-0.36.jar” #creating a loop for i in $INPUT_DIR/*$APPENDIX1 do FORWARD=$(basename…

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Accepted biojava-live 1:1.9.5+dfsg-1 (source all) into experimental, experimental

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Fri, 08 Apr 2022 21:21:13 +0200 Source: biojava-live Binary: libbiojava-java libbiojava-java-doc libbiojava1.9-java Architecture: source all Version: 1:1.9.5+dfsg-1 Distribution: experimental Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Pierre Gruet <p…@debian.org> Description: libbiojava-java – Java API to biological data and applications…

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[SpotBugs] htsjdk.samtools.cram.structure.CramHeader defines clone() but doesn’t implement Cloneable

Cloneable is not used very much so maybe deprecate and remove the clone() method? /cc @jmthibault79, @cmnbroad See spotbugs.readthedocs.io/en/stable/bugDescriptions.html#cn-class-defines-clone-but-doesn-t-implement-cloneable-cn-implements-clone-but-not-cloneable Part of #1267 Report: In class htsjdk.samtools.cram.structure.CramHeader In method htsjdk.samtools.cram.structure.CramHeader.clone() At CramHeader.java:[lines 80-85] Read more here: Source link

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What is ClustalW? Tutorial of How to Use ClustalW

Share Tweet Share Share Email ClustalW is a computer tool of significant importance in bioinformatics. Primarily, biologists and statisticians used it for multiple sequence alignment. Many versions of ClustalW over the development of the algorithm are available now. How to perform a search on ClustalW? ClustalW homepage 1. Go to…

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org.openapi.generator to Java client + model with oneOff in swagger

I’m currently enrolled with a spring-boot project, and they are using an API first approach which I think is great… except that this approach leads to us generating our ingoing API clients + input models, and the chosen tool org.openapi.generator 5.3.0 is really bad at it. I have an API…

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Trimmomatic/ linux system

Trimmomatic/ linux system 1 Hi all, I am trying to remove adapters and clean my RNA-seq.gz files using Trimmomatic, loaded on a Linux system (supercomputer server) Following the steps for Pair ends reads, explained in the manual (www.usadellab.org/cms/?page=trimmomatic) java -jar trimmomatic-0.39.jar PE input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True LEADING:3…

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How to merge multiple OpenAPI 3.0 specification files into one in Maven?

In a Maven project with Spring Boot, there are several OpenAPI 3.0 specification files. One spec defines all HTTP errors (errors.yml), and the components of errors.yml are referenced in other spec. I want to generate an output spec with all components of errors.yml inside. Input spec: schema: $ref: “errors.yml#/components/schemas/Error” Wished…

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google careers ADM

google data scientist certificate careers at google canada google applied jobs google hiring 2022 google ads specialist hiring hiring in google google company recruitment 2021 google frontend developer google reviewer job google philanthropy jobs machine learning developer google google bioinformatics jobs google android developer jobs google attorney jobs google pm…

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Install Jupyter Notebook on Debian 11 Bullseye Linux

Tutorial to learn the steps involve in the installation of Jupyter Notebook on Debian 11 Bullseye using command terminal. What is Jupyter Notebook? The Jupyter Project is a non-profit initiative that aims to develop and provide open-source software and open standards for interactive work. One of the most famous products…

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ChromatogramNonlinearScaler.Identity (biojava-legacy 1.9.2 API)

ChromatogramNonlinearScaler.Identity (biojava-legacy 1.9.2 API) JavaScript is disabled on your browser. Summary:  Nested |  Field |  Constr |  Method Detail:  Field |  Constr |  Method java.lang.Object org.biojava.bio.chromatogram.graphic.ChromatogramNonlinearScaler.Identity Method Summary Methods inherited from class java.lang.Object clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait Summary:  Nested |  Field |  Constr |  Method Detail:  Field |  Constr |  Method Copyright © 2020…

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SAMSequenceRecord

SAMSequenceRecord JavaScript is disabled on your browser. All Implemented Interfaces: java.io.Serializable, java.lang.Cloneable public class SAMSequenceRecord extends AbstractSAMHeaderRecord implements java.lang.Cloneable Header information about a reference sequence. Corresponds to @SQ header record in SAM text header. See Also: Serialized Form Field Summary Fields  Modifier and Type Field and Description static java.lang.String ASSEMBLY_TAG …

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Top 50 H20 interview questions and answers

H20 interview questions and answers 1) What is AutoML in H2O? H2O’s Automatic Machine Learning (AutoML) H2O is a fully open-source, distributed in-memory machine learning platform with linear scalability. … H2O AutoML can be used for automating the machine learning workflow, which includes automatic training and tuning of many models…

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net.sf.samtools.SAMFileHeader$GroupOrder java code examples | Tabnine

public void addAlignment(final SAMRecord alignment) { if (sortOrder.equals(SAMFileHeader.SortOrder.unsorted)) { if (!header.getGroupOrder().equals(SAMFileHeader.GroupOrder.none)) { throw new UnsupportedOperationException(“GroupOrder ” + header.getGroupOrder() + ” is not supported”); } writeAlignment(alignment); } else if (presorted) { assertPresorted(alignment); writeAlignment(alignment); } else { alignmentSorter.add(alignment); } } Read more here: Source link

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spring boot – How to make a synchronous call with WebClient using Open API Code Generator

Spring in RestTemplate documentation has note: As of 5.0 the class org.springframework.web.client.RestTemplate is in maintenance mode, with only minor requests for changes and bugs to be accepted going forward. Please, consider using the org.springframework.web.reactive.client.WebClient which has a more modern API and supports sync, async, and streaming scenarios docs.spring.io/spring-framework/docs/current/javadoc-api/org/springframework/web/client/RestTemplate.html When I…

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org.biojava.nbio.structure.PDBHeader.getRfree java code examples | Tabnine

mmtfDecoderInterface.setHeaderInfo(pdbHeader.getRfree(), pdbHeader.getRwork(), pdbHeader.getResolution(), pdbHeader.getTitle(), MmtfUtils.dateToIsoString(pdbHeader.getDepDate()), MmtfUtils.dateToIsoString(pdbHeader.getRelDate()), MmtfUtils.techniquesToStringArray(pdbHeader.getExperimentalTechniques())); mmtfDecoderInterface.setXtalInfo(MmtfUtils.getSpaceGroupAsString(xtalInfo.getSpaceGroup()), MmtfUtils.getUnitCellAsArray(xtalInfo), MmtfUtils.getNcsAsArray(xtalInfo.getNcsOperators())); Read more here: Source link

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Generate Server Code Using OpenAPI Generator

In this weblog, you’ll learn to generate server code utilizing the OpenAPI Generator based mostly on an OpenAPI specification. The code will likely be generated for a Spring Boot Application, however OpenAPI helps many different languages which can be utilized. 1. Introduction In November I attended JFall, the biggest sooner…

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MetricsFile

All Methods Static Methods Instance Methods Concrete Methods  Modifier and Type Method and Description void addAllMetrics(java.lang.Iterable<BEAN> beanz) Add multiple metric beans at once. void addHeader(Header h) Adds a header to the collection of metrics. void addHistogram(Histogram<HKEY> histogram) Adds a histogram to the list of histograms in the metrics file. void addMetric(BEAN bean) Adds a bean to the…

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java – GATK: HaplotypceCaller IntelPairHmm only detecting 1 thread

I can’t seem to get GATK to recognise the number of available threads. I am running GATK (4.2.4.1) in a conda environment which is part of a nextflow (v20.10.0) pipeline I’m writing. For whatever reason, I cannot get GATK to see there is more than one thread. I’ve tried different…

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File: reproducible.patch | Debian Sources

123456789101112131415 Author: Chris West <solo-debianbugs@goeswhere.com> Last-Update: Sun, 9 Apr 2017 17:36:01 UTC Bug-Debian: bugs.debian.org/859958 Description: make build reproducible — a/build.xml +++ b/build.xml @@ -403,6 +403,7 @@ doctitle=”${Name.biojava}-${version}” maxmemory=”512m”> <link href=”http://java.sun.com/j2se/1.5.0/docs/api/” offline=”false”/> + <arg value=”-notimestamp”/> <group title=”Core biological packages” packages=”org.biojava.bio:org.biojava.bio.dist:org.biojava.bio.search:org.biojava.bio.seq:org.biojava.bio.seq.db:org.biojava.bio.seq.genomic:org.biojava.bio.seq.io:org.biojava.bio.symbol:org.biojava.bio.alignment:org.biojava.directory:org.biojava.bibliography:org.biojava.bio.taxa:org.biojava.bio.seq.filter” /> Read more here: Source link

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V1DaemonSet – client-java-api 10.0.1 javadoc

Latest version of io.kubernetes:client-java-api javadoc.io/doc/io.kubernetes/client-java-api Current version 10.0.1 javadoc.io/doc/io.kubernetes/client-java-api/10.0.1 package-list path (used for javadoc generation -link option) javadoc.io/doc/io.kubernetes/client-java-api/10.0.1/package-list Read more here: Source link

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Mapping to multiple references using bbmap

So my question comes in two parts: First of all is what I’m trying to do within reason given the tools I am using? I am investigating the shuffling effects of a recombinase on a known reporter sequence which subsequently generates libraries of unique sequences. By simulating all of the…

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Urgent mini project: Creat plot in R with ggplot | R Programming Language | Statistics

Use ggplot to create a plot in R. The plot should look exactly like the sketch attached. Here is the data: X <- c(0,3) HighMP <- c(-0.021248, 0.02615) LowMP <- c(-0.001879, -0.008904) Please use Times New Roman as font for the plot. The font size should be adjustable. The color…

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GATK HaplotypeCaller with interval list

I am trying to use the -L option of GATK HaplotypeCaller to call SNPs and short InDels with in an interval list. My interval list file (top8snp.interval_list) content is as follows: 12 33029845 33030845 + rs24767598 13 40586682 40587682 + rs24748362 18 24373857 24374857 + rs8856159 21 50381146 50382146 +…

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Comparing Compiled and Interpreted Programming Languages

Only binary code can be understood and executed by computers. High–programmers use level programming languages like C, C++, Python, and Java. Because they mimic human languages and mathematical notation, such languages are easier to work with. On the other hand, Computers are unable to execute code written in a high–level…

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Senior Bioinformatics Software Developer – Bethesda

Medical Science & Computing, (MSC), a Dovel company, is seeking skilled Senior Bioinformatics Software Developers to join our team supporting our client, NCBI at the National Institutes of Health, (NIH) in Bethesda, MD. The National Center for Biotechnology Information (NCBI) is part of the National Library of Medicine (NLM) at…

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Efficiently merge two BAM files while retaining reads from only one file in overlapping regions

Efficiently merge two BAM files while retaining reads from only one file in overlapping regions 1 I have a WGS BAM file that is fairly large (>150GB) and a smaller BAM file (<5GB) with reads in a small 10Mbp region. I want to (efficiently) merge the two BAM files while…

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variant – Error running gatk HaplotypeCaller with allele specific annotations

I’ve got HaplotypeCaller working nicely in standard mode, like so: # Run haplotypcaller gatk –java-options “-Xmx4g” HaplotypeCaller –intervals “$INTERVALS” -R “$REF” -I “$OUT”/results/alignment/${SN}_sorted_marked_recalibrated.bam -O “$OUT”/results/variants/${SN}_g.vcf.gz -ERC GVCF But when I try in allele-specific mode, I get the following error. All I’ve done is add the -G annotations at the end,…

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H2O is an in-memory platform for distributed, scalable machine learning

H2O is an in-memory platform for distributed, scalable machine learning. H2O uses familiar interfaces like R, Python, Scala, Java, JSON and the Flow notebook/web interface, and works seamlessly with big data technologies like Hadoop and Spark. H2O provides implementations of many popular algorithms such as Generalized Linear Models (GLM), Gradient…

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LargeBuffer (BioJava-1.4 API)

LargeBuffer (BioJava-1.4 API) org.biojava.utils.io Class LargeBuffer java.lang.Object org.biojava.utils.io.LargeBuffer public class LargeBuffer extends Object Wrapper arround MappedByteBuffers to allow long-indexed access to files larger than 2 gigs. Author: Matthews Pocock   Method Summary  void force()              byte get()              byte get(long pos)              char getChar()              char getChar(long pos)              double getDouble()            …

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repo/gentoo.git – Official Gentoo ebuild repository

dev-java/cpptasks: Fix Javadoc generation on JDK 11+HEADmaster The ‘javadoc’ program shipped in JDK 11+ requires all classes used by the input source files to be present in the classpath passed to it. This has caused numerous other bugs alike, including 780531, 788109, and 820863. Closes: bugs.gentoo.org/831294 Signed-off-by: Yuan Liao <liaoyuan@gmail.com>…

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java – OpenApi Generator to generate parameter with @RequestBody as String

I have the following OpenApi specs: paths: /student: post: requestBody: required: true content: application/json: schema: $ref: “#/components/schemas/Student” responses: 204: components: schemas: Student: type: object properties: name: type: string school: type: string With org.openapitools.generator, it generates a controller with function like below void addStudent(@RequestBody Student student) { } Is there any…

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Question: total memory usage (–mem) exceeded the RealMemory in pcluster with SLURM

Hello, I have set RealMemory=58000 (though they are 64G instances) in the file slurm_parallelcluster_queue_partition.conf When I run the following commands: sbatch -N 1 -n 1 –mem=40000 –wrap=”srun script.sh first_task” sbatch -N 1 -n 1 –mem=40000 –wrap=”srun script.sh second_task” and more They will be assigned to single instance which lead to…

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How to convert a string to an inputstream in Bioclipse javascript editor?

In this situation we have to fall back to Java. You are trying to call the method ui.save which according to man ui.save looks like this: > man ui.save ——————————————— ui.save(String filePath, InputStream content) ——————————————— Save the content of the InputStream to the given path. So this method wants an…

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bioinformatics-data – Github Help

0 1 0 bioinformatics-data,An old Phylogenetik Project (2007) in JAVA, with (some) phylogeny, bioinformatics algorithms, matrix implementations and comparisons, PAM and BLOSUM (extract from gabriel.chandesris.free.fr/projets/Phylogenetik/ ) User: gabywald Home Page: gabriel.chandesris.free.fr/projets/Phylogenetik/ java bioinformatics biology javaswing bioinformatics-tool bioinformatics-algorithms bioinformatics-data student-project student-work student Read more here: Source link

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Trimmomatic parameters

Trimmomatic parameters 0 $java -jar /apps/eb/Trimmomatic/0.39-Java-1.8.0_144/trimmomatic-0.39.jar PE -phred33 seq1_L2_1.fq.gz seq1_L2_2.fq.gz _L2_r1_paired_fq.gz seq1_L2_r1_unpaired.fq.gz seq_L2_r2_paired.fq.gz Seq1_L2_r2_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:5 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:5 Trimmomatic • 137 views • link updated 15 hours ago by GenoMax 110k • written 17 hours ago by ronny • 0 Login before adding your…

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Rockhopper’s alignment issue

Rockhopper’s alignment issue 0 Hi everyone, I’m trying to identify the operons with the Rockhopper tool but at the end of the alignment something strange happens: Aligning sequencing reads from file: SRR6757591_1.sorted.bam Total reads: 10209877 Successfully aligned reads: 9358027 92% (>NC_000913.3 Escherichia coli str. K-12 substr. MG1655, complete genome) Aligning…

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MCScanX: not found – githubmate

Hi CJ-Chen, Thanks for developing this tool. I having an issue when I try to use Quick Run MCScanX Wrapper. error log here: [Debug…All Standard Error Info will show as following:…] Curr log file:/tmp/TBtools.14595798488989250861.20210723103734.log Curr java version:11.0.11 Curr TBtools version:1.09854 Maxmum Memory for Curr TBtools: 4162846720 curVersion:1.09854:force Fetch Location:200 Factor:0.1516546094367225…

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Trying to trim last bp of several samples with BBduk at once

Trying to trim last bp of several samples with BBduk at once 1 Hi, I am trying to use BBduk to trim back my 151bp sequences to 150bp. I tried to create a loop for this so I could do one entire pool at the time, but I do not…

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Roche hiring Principal Bioinformatics Scientist I in Santa Clara, California, United States

Impact Healthcare Roche Sequencing is developing ground-breaking next-generation sequencing (NGS) products that allow scientists/clinicians powerful new avenues to investigate DNA, the blueprint of any lifeforms, in days enabling them to understand health conditions such as cancer, HIV, COVID19 and more! We are not only changing science but changing lives through…

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Problem with viewing BAM files in IGV

Problem with viewing BAM files in IGV 1 Hi everyone, I’m quite new to bioinformatics and I’m having some beginner problems with IGV. I’ve got some BAM files that were generated using the GATK best practice pipeline for SNP discovery, with BAI files located in the same directory. I’m using…

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