Ethan Willie summarizes his 8-month contribution to the Genome Sciences Centre, where he worked on several pipelines including ABySS, Trans-ABySS, and Genome-Validator. He validated tools like ChimeraScan, hg38 annotations, Trinity, and Manta. Willie analyzed multiple projects, developed scripts to improve workflows, and learned skills in bioinformatics problem-solving, scripting, visualization, and presentation. He acknowledges areas for improvement like troubleshooting and public speaking, and hopes to further develop his genomics skills and apply his experience in future roles.
Standardising Swedish genomics analyses using nextflowPhil Ewels
The SciLifeLab National Genomics Infrastructure is one of the largest sequencing facilities in Europe. We are an accredited facility providing library preparation, sequencing, basic analysis and quality control for Swedish research groups. Our sample throughput requires a highly automated and robust bioinformatics platform. Until recently, we had multiple analysis pipelines built with a range of different workflow tools for each data type. This made development work difficult and led to inevitable technical debt. In this talk I will describe how we have migrated to Nextflow for a range of our data types, the difficulties that we faced and how we hope to leverage Nextflow to migrate to the cloud in coming years.
Tips for Writing Better Charters for Exploratory Testing Sessions by Michael...TEST Huddle
We will look at some common pitfalls encountered when chartering your testing for session-based exploratory testing. After a brief overview of the session-based test management process we will jump into specific practices and techniques to help you and the rest of your team achieve better coverage and find better bugs. A presentation for the EuroSTAR Software Testing Community from September 2012.
Standardising Swedish genomics analyses using nextflowPhil Ewels
The SciLifeLab National Genomics Infrastructure is one of the largest sequencing facilities in Europe. We are an accredited facility providing library preparation, sequencing, basic analysis and quality control for Swedish research groups. Our sample throughput requires a highly automated and robust bioinformatics platform. Until recently, we had multiple analysis pipelines built with a range of different workflow tools for each data type. This made development work difficult and led to inevitable technical debt. In this talk I will describe how we have migrated to Nextflow for a range of our data types, the difficulties that we faced and how we hope to leverage Nextflow to migrate to the cloud in coming years.
Tips for Writing Better Charters for Exploratory Testing Sessions by Michael...TEST Huddle
We will look at some common pitfalls encountered when chartering your testing for session-based exploratory testing. After a brief overview of the session-based test management process we will jump into specific practices and techniques to help you and the rest of your team achieve better coverage and find better bugs. A presentation for the EuroSTAR Software Testing Community from September 2012.
Testing for agile teams . What's the difference between this and other testing ? What are the goals for such testing ?
Is agile testing needed at all ? Why ?
You will find some answers inside and mist likely will be directed to the right way.
VIP Workshop: Effective Habits of Development TeamsPaul Schreiber
There’s so many tools out there, but what are the best for managing development teams? Paul Schreiber, Developer at FiveThirtyEight, will walk through best practices and tools for workflow, automation and testing, along with good practices for managing development teams.
"Finding Bad Needles on a Worldwide Scale" - presentation on our experience of developing, testing and improving cross-site scripting scanners and the methods of more accurate web application security testing. See 2015.appsec.eu for more information.
Examines some of the fundamental problems with the way the industry thinks about software "engineering", and breaks some notions in order to find useful ways of improving your code quality, and your skills and discipline as a developer.
Software Testing Training : Tonex TrainingBryan Len
Software testing preparing shows you the propelled software testing and standards for the present thorough testing request and gives you the ground-breaking instrument and strategy to lessen software absconds, enhance the quality and upgrade your business achievement.
Audience :
IT professionals, Software testers, Test analysts,Project managers, quality managers, software development managers, business analysts or IT directors, Software developers , Executives and managers of software testing area and more.
Training objectives:
Understand Fundamentals of software testing
Necessary mathematical knowledge of software testing
Explain different phases of software life cycle
Understand static software testing techniques
Develop software test design techniques
Manage the software testing procedures
Recognize different types of software testing and apply the appropriate method for different software testing challenges
Apply testing tools for mobile systems
Carry out the functional and usability testing to software
Test the software through web, computer or mobile systems
Training outlines:
Introduction to Software Testing
Graph Theory Basics for Software Testers
Software Development Life Cycle
Distributions and Data Analysis
Software Testing Strategy
Static Software Testing
Usability Testing
Data Flow Testing
Data Flow Testing
Functional Testing
Software Testing Design Techniques
Software Testing Management
Hands On, Workshops, and Group Activities
Sample Workshops and Labs for Software Testing Training
The software testing course by TONEX is intuitive course with a considerable measure of class talks and activities planning to give you a valuable asset to software testing. This preparation primarily centers around lessening the holes between the software creation and what true needs. Along these lines, software testing must be put into the early period of the starting figuring with the goal that it can help experts for their software improvement vocations.
Request for more information. Visit Tonex training website links below
Software Testing Training
https://www.tonex.com/training-courses/software-testing-training/
Presentation from HiPC'18 (https://arxiv.org/abs/1805.01177).
Abstract:
Given the cost of HPC clusters, making best use of them is crucial to improve infrastructure ROI. Likewise, reducing failed HPC jobs and related waste in terms of user wait times is crucial to improve HPC user productivity (aka human ROI). While most efforts (e.g.,debugging HPC programs) explore technical aspects to improve ROI of HPC clusters, we hypothesize non-technical (human) aspects are worth exploring to make non-trivial ROI gains; specifically, understanding non-technical aspects and how they contribute to the failure of HPC jobs.
In this regard, we conducted a case study in the context of Beocat cluster at Kansas State University. The purpose of the study was to learn the reasons why users terminate jobs and to quantify wasted computations in such jobs in terms of system utilization and user wait time. The data from the case study helped identify interesting and actionable reasons why users terminate HPC jobs. It also helped confirm that user terminated jobs may be associated with non-trivial amount of wasted computation, which if reduced can help improve the ROI of HPC clusters.
Testing for agile teams . What's the difference between this and other testing ? What are the goals for such testing ?
Is agile testing needed at all ? Why ?
You will find some answers inside and mist likely will be directed to the right way.
VIP Workshop: Effective Habits of Development TeamsPaul Schreiber
There’s so many tools out there, but what are the best for managing development teams? Paul Schreiber, Developer at FiveThirtyEight, will walk through best practices and tools for workflow, automation and testing, along with good practices for managing development teams.
"Finding Bad Needles on a Worldwide Scale" - presentation on our experience of developing, testing and improving cross-site scripting scanners and the methods of more accurate web application security testing. See 2015.appsec.eu for more information.
Examines some of the fundamental problems with the way the industry thinks about software "engineering", and breaks some notions in order to find useful ways of improving your code quality, and your skills and discipline as a developer.
Software Testing Training : Tonex TrainingBryan Len
Software testing preparing shows you the propelled software testing and standards for the present thorough testing request and gives you the ground-breaking instrument and strategy to lessen software absconds, enhance the quality and upgrade your business achievement.
Audience :
IT professionals, Software testers, Test analysts,Project managers, quality managers, software development managers, business analysts or IT directors, Software developers , Executives and managers of software testing area and more.
Training objectives:
Understand Fundamentals of software testing
Necessary mathematical knowledge of software testing
Explain different phases of software life cycle
Understand static software testing techniques
Develop software test design techniques
Manage the software testing procedures
Recognize different types of software testing and apply the appropriate method for different software testing challenges
Apply testing tools for mobile systems
Carry out the functional and usability testing to software
Test the software through web, computer or mobile systems
Training outlines:
Introduction to Software Testing
Graph Theory Basics for Software Testers
Software Development Life Cycle
Distributions and Data Analysis
Software Testing Strategy
Static Software Testing
Usability Testing
Data Flow Testing
Data Flow Testing
Functional Testing
Software Testing Design Techniques
Software Testing Management
Hands On, Workshops, and Group Activities
Sample Workshops and Labs for Software Testing Training
The software testing course by TONEX is intuitive course with a considerable measure of class talks and activities planning to give you a valuable asset to software testing. This preparation primarily centers around lessening the holes between the software creation and what true needs. Along these lines, software testing must be put into the early period of the starting figuring with the goal that it can help experts for their software improvement vocations.
Request for more information. Visit Tonex training website links below
Software Testing Training
https://www.tonex.com/training-courses/software-testing-training/
Presentation from HiPC'18 (https://arxiv.org/abs/1805.01177).
Abstract:
Given the cost of HPC clusters, making best use of them is crucial to improve infrastructure ROI. Likewise, reducing failed HPC jobs and related waste in terms of user wait times is crucial to improve HPC user productivity (aka human ROI). While most efforts (e.g.,debugging HPC programs) explore technical aspects to improve ROI of HPC clusters, we hypothesize non-technical (human) aspects are worth exploring to make non-trivial ROI gains; specifically, understanding non-technical aspects and how they contribute to the failure of HPC jobs.
In this regard, we conducted a case study in the context of Beocat cluster at Kansas State University. The purpose of the study was to learn the reasons why users terminate jobs and to quantify wasted computations in such jobs in terms of system utilization and user wait time. The data from the case study helped identify interesting and actionable reasons why users terminate HPC jobs. It also helped confirm that user terminated jobs may be associated with non-trivial amount of wasted computation, which if reduced can help improve the ROI of HPC clusters.
2. OVERVIEW
• Pipelines
• Projects
• Validation(s)
• ChimeraScan
• Trinity
• Manta
• Development
• Additional Work
• What I learned
• What I can improve
• Moving forward
• Acknowledgments
3. Pipelines
• ABySS: Assemble short reads by a de novo, parallel, paired-end sequence assembler
• Trans-ABySS: Analyze assemblies for structural variants and splice variants
using a reference genome and annotations.
• Genome-Validator: Validate fusion and indel events from Trans-ABySS
against given BAM files and attempt to assigning ‘tumourigenicity’ as ‘somatic’
or ‘germline’ to events when both a normal tumour genome are given.
• Delly: Discover split-read and paired-end structural variants and genotyping
from parallel sequencing data.
• Microbial Detection Pipeline: Detect bacterial and/or viral sequences to
determine potential contamination or integration into the genome.
• Integration Site Pipeline: Detect putative integrative sites of viral sequences
into human sequences.
• Probing Pipeline: Detect fusion and SNP mutations in genome and
transcriptome libraries.
• Compression and Transfer: Compress and transfer files off of scratch space
for archiving and reducing total space usage on scratch space.
6. ChimeraScan-0.4.5
A software package that detects gene fusions in paired-end RNA
sequencing (RNA-Seq) datasets. differs from other fusion finders(deFUSE)
in that it adds a fragmentation step along with the whole paired-end
approach which is also used by deFUSE.
Script(s):
• setup:
– /projects/trans_scratch/software/chimerascan/scripts/chimerascan_setup_final.sh
• checker:
– /projects/trans_scratch/software/chimerascan/scripts/chimerascan_checker.sh
• cleaner:
– /projects/trans_scratch/software/chimerascan/scripts/chimerascan_cleaner.sh
• binner:
– /projects/trans_scratch/software/chimerascan/scripts/binning_beta.py
• summarizer:
– /projects/trans_scratch/software/chimerascan/scripts/chimerascan.sum.sh
• report generator:
– /projects/trans_scratch/software/chimerascan/scripts/ChimeraScan.report.sh
7. Manta
Rapid detection of structural variants and indels for clinical sequencing
applications
Script(s):
• manta_sum.sh:
– /home/ewillie/tools/scripts/manta_sum.sh
• manta_delly_overlay.py:
– /home/ewillie/tools/scripts/manta_delly_overlay.py
• Manta_gv2_overlay.py:
– /home/ewillie/tools/scripts/manta_gv2_overlay.py
• vcfToBedpe:
– /projects/trans_scratch/software/svtools-Manta2Bedpe/vcfToBedpe
9. Additional Work
• Assemblies: Run ABySS to assemble sample(s) for further downstream analyzing.
• Analyses: Run various analysis tools on data and comparing their result by means of
overlays and/or visualization.
• Overlays: Compare results between different tools or different settings to find
similarities and differences. The overlays are done using appropriate scripts, and venn
diagrams are generated to help illustrate similarities and/or differences.
• Testing Scripts: new scirpts such as integration_pipeline.sh were tested for potential
bugs and ease of use. Testing was done iteratively, with each iteration providing more
confidence.
• ChimeraScan Wiki: Create a comprehensive wiki with information regarding
validation, and a detailed procedure for running the tool. Additional information
such as installation procedure, resource requirements, and interpreting the
outputs. The wiki also contains debugging information.
11. What I Learned
• Real world applications of bioinformatics.
• Problem solving including troubleshooting, debugging and querying the
literature.
• Bash scripting language including a significant knowledge of terminal
commands.
• Writing scripts to improve time and efficiency of jobs.(Do a job manually
for > 2hrs or write a script to do it in a fraction of that time.)
• A greater attention to detail to help reduce rate of errors.
• Time management, task prioritization and meeting deadlines.
• Visualize and analyzing structural variants using IGV.
12. What I could work on
Problem solving and troubleshooting skills.
Deeper understanding of the SVIA pipeline tools.
Clear and concise presentation of my results.
Minimizing my rate of error when performing tasks.
Verbal presentation skills.
Create an appetite for personal projects.
ANY SUGGESTIONS????????
13. Moving Forward
My interest in the algorithmic aspect of genomics has grown tremendously,
enticing me to take more applied algorithm courses.
Obtaining a genomics certificate as part of my degree to further develop my
interest in genomic sciences.
Since i am now aware of the qualities and skills that are needed to be successful
in this rapidly changing industry, I will be dedicating time to further develop
these qualities and sharpen these skills.
Improving my scripting abilities both in python and bash to build on the
experience I have already gained here during the last eight months.
Applying the knowledge and skills i have acquired here in order to be successful
in a different work environment.