Please join us on Tuesday May 19 for an online training on the Ingenuity Pathways Analysis (IPA).
Learn how you can leverage Ingenuity IPA’s expert curation of the scientific literature from the past 18+ years and the thousands of hours spent to validate and organize NGS data from sources such as the SRA database, GEO, TCGA and more. Researchers can easily analyze their own NGS data alongside public datasets and manual curation of literature to identify the best testable hypotheses, targets and biomarkers.
Training Agenda
Time: Tuesday, May 19th, 10am-12:30pm Zoom Web Training
Presenter: Devendra Mistry, PhD, Field Application Scientist
10-10:15am: Introduction to IPA Database and Applications Supported
10:15-11:00am: Live demo of IPA Analysis Workflow
• Format, upload your data, and launch an analysis
• Identify pathways associated with your gene/protein/metabolite list
• Find causal regulators and their directional effect on genes functions and diseases
11:30 -1pm: Advanced IPA Analysis Topics
• Build pathways, make connections between entities, and overlay multiple dataset
• Multi-groups (treatments, time points etc.) and multi-omic comparisons
o How the pathways, biological processes and regulators are regulated across different time points, treatments, disease conditions?
o Generating a list of biomarkers specific to a condition
• How to gain insights from public data using Analysis Match and Activity Plot
o Compare user analysis with analyses of public datasets from GEO, SRA, TCGA etc.
o How is the regulator, pathway, biological function of interest behaving across ~60,000 public dataset analyses
Please follow the link below to register for this training:
https://usc.qualtrics.com/jfe/form/SV_0cZIV5DwfXuaOhf
Let us know if you have any questions.
USC Libraries Bioinformatics Services
https://libraries.usc.edu/bioinformatics
nmlbio@usc.edu
Showing posts with label bioinformatics. Show all posts
Showing posts with label bioinformatics. Show all posts
Monday, May 11, 2020
Monday, April 13, 2020
Bioinformatics Self-learning Resources Guide
The USC Libraries Bioinformatics Services is pleased to announce the availability of the Bioinformatics Self-learning Resources Guide as part of our ongoing efforts to support the COVID-19 Research Continuity Plan by the university as well as by the Keck School of Medicine.
This Bioinformatics Self-learning Resources Guide has been compiled for students and researchers who are interested in learning how to carry out some of the most common bioinformatics tasks. This resource provides links to our previous workshops and training on our licensed commercial bioinformatics software. It also includes the links to our hand-picked list of high-quality publicly accessible bioinformatics tutorials and webinars from other institutions, focusing on open-source tools.
We will continue to update this resources guide and we welcome any comments and suggestions.
Stay safe and healthy!
USC Libraries Bioinformatics Services
nmlbio@usc.edu
https://libraries.usc.edu/bioinformatics
This Bioinformatics Self-learning Resources Guide has been compiled for students and researchers who are interested in learning how to carry out some of the most common bioinformatics tasks. This resource provides links to our previous workshops and training on our licensed commercial bioinformatics software. It also includes the links to our hand-picked list of high-quality publicly accessible bioinformatics tutorials and webinars from other institutions, focusing on open-source tools.
We will continue to update this resources guide and we welcome any comments and suggestions.
Stay safe and healthy!
USC Libraries Bioinformatics Services
nmlbio@usc.edu
https://libraries.usc.edu/bioinformatics
Monday, March 30, 2020
Analyzing single-cell RNAseq data in Partek Flow--Webinar on Thursday April 2nd
Partek Flow has a powerful workflow for single-cell RNAseq data analysis. If you have or will have single-cell RNA-seq data soon, we strongly recommend that you sign up for next Thursday April 2nd webinar, select the Boston session, which starts at 11:15 AM LA time.
Three Sessions to Choose From:
April 1, 2020, 2:15 p.m. SGT (Singapore)
April 2, 2020, 2:15 p.m. BST (London)
April 2, 2020, 2:15 p.m. EDT (Boston)
Same content in all sessions
Tissue transcriptomics is a family of techniques designed to allow transcriptomic profiling of cells within a tissue. It has gained a lot of attention over the past two years and is paralleling and extending advances made in single cell RNA-Seq technology.
Join us for a webinar where we will demonstrate the analysis of 10x Visium data in Partek Flow software. You will learn how to leverage its statistical power to answer your biological questions and see exciting new features in the Partek Flow Data Viewer.
What you will learn:
• Import 10x Genomics spatial transcriptomics data
• Combine gene expression data with histological information
• Identify clusters of spots based on gene expression profiles
• Perform differential gene expression
Three Sessions to Choose From:
April 1, 2020, 2:15 p.m. SGT (Singapore)
April 2, 2020, 2:15 p.m. BST (London)
April 2, 2020, 2:15 p.m. EDT (Boston)
Same content in all sessions
Tissue transcriptomics is a family of techniques designed to allow transcriptomic profiling of cells within a tissue. It has gained a lot of attention over the past two years and is paralleling and extending advances made in single cell RNA-Seq technology.
Join us for a webinar where we will demonstrate the analysis of 10x Visium data in Partek Flow software. You will learn how to leverage its statistical power to answer your biological questions and see exciting new features in the Partek Flow Data Viewer.
What you will learn:
• Import 10x Genomics spatial transcriptomics data
• Combine gene expression data with histological information
• Identify clusters of spots based on gene expression profiles
• Perform differential gene expression
Monday, March 23, 2020
An important update on our bioinformatics services
As part of USC Libraries’ COVID-19 responses, our offices on both HSC and UPC will be closed starting Monday March 16 and possibly 'til April 13. However, the USC Libraries Bioinformatics Services will continue to deliver the quality bioinformatics support you have come to expect during this period of time as we will be working from home. While the in-person consultation will not be available, all of your questions and requests will be addressed in a timely manner via emails and online platforms such as the Zoom. All our bioinformatics computing resources will be operating as usual to support your sequencing data analysis needs.
1. For general inquiries and request, email nmlbio@usc.edu.
2. For consultation request: https://uschsl.co1.qualtrics.com/jfe/form/SV_di1fbQJYL4QsxXD
3. For NGS data analysis request: https://uschsl.co1.qualtrics.com/jfe/form/SV_8GHy25wi20UsL2Z
4. Whenever necessary, Zoom meeting will be arranged between 10 am and 4 pm, Monday to Friday.
Please take a good care of yourself, everyone!
Fight on!
Yibu, Meng, and Eddie
USC Libraries Bioinformatics Services
nmlbio@usc.edu
libraries.usc.edu/bioinformatics
1. For general inquiries and request, email nmlbio@usc.edu.
2. For consultation request: https://uschsl.co1.qualtrics.com/jfe/form/SV_di1fbQJYL4QsxXD
3. For NGS data analysis request: https://uschsl.co1.qualtrics.com/jfe/form/SV_8GHy25wi20UsL2Z
4. Whenever necessary, Zoom meeting will be arranged between 10 am and 4 pm, Monday to Friday.
Please take a good care of yourself, everyone!
Fight on!
Yibu, Meng, and Eddie
USC Libraries Bioinformatics Services
nmlbio@usc.edu
libraries.usc.edu/bioinformatics
Monday, October 28, 2019
Monday, October 21, 2019
Post-doc and Bioinformatician positions available in NYC
The Bunyavanich Lab welcomes talented, self-motivated individuals who can fulfill the responsibilities and requirements below to apply for positions in our lab at the Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY. The successful applicant will be part of an interdisciplinary team led by Dr. Supinda Bunyavanich that applies computational analysis and bioinformatics to interpret multi-scale data generated from subjects with asthma and allergic diseases. Our researchers receive generous packages, including robust salaries and a wealth of opportunities to participate in academic activities here at the Institute for Data Science and Genomic Technology and more broadly at regional and national workshops and conferences. We are located in the heart of Manhattan, and Mount Sinai is one of the oldest and largest teaching hospitals in the US.
Responsibilities:
• Analyze high-throughput sequence data.
• Develop and implement methods to analyze these data.
• Maintain large datasets linked to clinical data.
• Communicate progress with PI regularly and contribute to the success of the research team.
• Develop and maintain productive collaborations within Mount Sinai and with outside researchers in academia and industry.
• Publish and present novel research findings in academic journals and conferences
• Some supervision of trainees and technical staff may also be required.
Requirements:
• Degree in bioinformatics, computer science, computational biology, genomics, or a related field.
• Outstanding programming skills in R, Python, and Unix shell scripting.
• Excellent track record of analyzing sequence data. Experience with clinical cohorts and microbiome analysis a plus.
• Demonstrated knowledge of statistics and statistical genetics. Familiarity with genomic data tools, repositories, and databases.
• Strong attention to detail and solid analytical skills.
• Ability to work hard and independently while contributing to the team effort and adhering to deadlines.
• Excellent oral and written communication skills with track record of productive collaborations.
• Demonstrated ability to work concurrently on several projects, and good understanding of analytic complexities to do independent research as well as assist other researchers.
The Institute for Data Science and Genomic Technology at the Icahn School of Medicine at Mount Sinai seeks to comprehensively integrate the digital universe of information into research, training, and patient care and to develop programs that advance the future of healthcare and data science.
Interested and qualified candidates should submit a CV and detailed letter of interest to Dr. Supinda Bunyavanich (Supinda.Bunyavanich at mssm.edu).
Responsibilities:
• Analyze high-throughput sequence data.
• Develop and implement methods to analyze these data.
• Maintain large datasets linked to clinical data.
• Communicate progress with PI regularly and contribute to the success of the research team.
• Develop and maintain productive collaborations within Mount Sinai and with outside researchers in academia and industry.
• Publish and present novel research findings in academic journals and conferences
• Some supervision of trainees and technical staff may also be required.
Requirements:
• Degree in bioinformatics, computer science, computational biology, genomics, or a related field.
• Outstanding programming skills in R, Python, and Unix shell scripting.
• Excellent track record of analyzing sequence data. Experience with clinical cohorts and microbiome analysis a plus.
• Demonstrated knowledge of statistics and statistical genetics. Familiarity with genomic data tools, repositories, and databases.
• Strong attention to detail and solid analytical skills.
• Ability to work hard and independently while contributing to the team effort and adhering to deadlines.
• Excellent oral and written communication skills with track record of productive collaborations.
• Demonstrated ability to work concurrently on several projects, and good understanding of analytic complexities to do independent research as well as assist other researchers.
The Institute for Data Science and Genomic Technology at the Icahn School of Medicine at Mount Sinai seeks to comprehensively integrate the digital universe of information into research, training, and patient care and to develop programs that advance the future of healthcare and data science.
Interested and qualified candidates should submit a CV and detailed letter of interest to Dr. Supinda Bunyavanich (Supinda.Bunyavanich at mssm.edu).
Sunday, April 29, 2018
[Bioinformatics Lunch Series] NGS Data Analysis with Partek Flow, May 4 2018
The USC Libraries Bioinformatics Service is pleased to present a four-workshop series on next generation sequencing (NGS) studies, addressing key issues from experiment design to functional interpretation of NGS results.
NGS Workshop #2-- “NGS Data Analysis with Partek Flow”
Featuring live-demos of Partek Flow and a primary focus on RNA-Seq workflow, this workshop covers the following topics:
• University-wide access of bioinformatics computing for NGS data analysis
• Essential guide to RNA-seq workflow
• Quick overview of Partek Flow’s other data analysis workflows for:
• Single-cell RNA-seq
• ChIP-seq
• DNA-seq
Time Noon - 1 pm, Friday, May 4th
Locations
1. Health Science Campus
West Conference Room, Norris Medical Library
2. University Park Campus (via livestreaming)
Learning Center, Wilson Dental Library (DEN21)
Lunch will be provided at both locations. Link to the livestreaming for private viewing is also available.
Sign up is mandatory:
https://uschsl.co1.qualtrics.com/jfe/form/SV_en6WeMXux2BI56J
Upcoming NGS study workshops:
#3 (May 15th)—Making sense of RNA-Seq data Part 1—Downstream effect analysis (pathways, diseases etc.)
#4 (June 7th)—Making sense of RNA-Seq data Part 2—Upstream regulation analysis (transcription factors etc.)
This workshop is part of the ongoing Bioinformatics Lunch Series, funded by USC Libraries Dean’s Challenge Grant.
Please let us know if you have any questions.
USC Libraries Bioinformatics Service
nmlbio@usc.edu
https://nml.usc.edu/bioinformatics
NGS Workshop #2-- “NGS Data Analysis with Partek Flow”
Featuring live-demos of Partek Flow and a primary focus on RNA-Seq workflow, this workshop covers the following topics:
• University-wide access of bioinformatics computing for NGS data analysis
• Essential guide to RNA-seq workflow
• Quick overview of Partek Flow’s other data analysis workflows for:
• Single-cell RNA-seq
• ChIP-seq
• DNA-seq
Time Noon - 1 pm, Friday, May 4th
Locations
1. Health Science Campus
West Conference Room, Norris Medical Library
2. University Park Campus (via livestreaming)
Learning Center, Wilson Dental Library (DEN21)
Lunch will be provided at both locations. Link to the livestreaming for private viewing is also available.
Sign up is mandatory:
https://uschsl.co1.qualtrics.com/jfe/form/SV_en6WeMXux2BI56J
Upcoming NGS study workshops:
#3 (May 15th)—Making sense of RNA-Seq data Part 1—Downstream effect analysis (pathways, diseases etc.)
#4 (June 7th)—Making sense of RNA-Seq data Part 2—Upstream regulation analysis (transcription factors etc.)
This workshop is part of the ongoing Bioinformatics Lunch Series, funded by USC Libraries Dean’s Challenge Grant.
Please let us know if you have any questions.
USC Libraries Bioinformatics Service
nmlbio@usc.edu
https://nml.usc.edu/bioinformatics
Sunday, April 8, 2018
[Bioinformatics Lunch Series] Key Considerations for NGS Experimental Design, April 18 2018
The USC Libraries Bioinformatics Service is pleased to present a four-workshop series on next generation sequencing (NGS) studies, addressing key issues from experiment design to functional interpretation of NGS results.
NGS Workshop #1-- “Key Considerations for NGS Experimental Design”
With a primary focus on RNA-Seq experiments, this workshop covers the following topics:
• Proper number of replicates
• Optimal sequencing depth
• Appropriate read type and length
• Quick points on designing single-cell RNA-Seq, ChIP-Seq, and DNA-Seq experiments
• Find the right sequencing service providers
Time Noon - 1 pm, Wednesday, April 18th
Locations
1. Health Science Campus
West Conference Room, Norris Medical Library
2. University Park Campus (via livestreaming)
Learning Center, Wilson Dental Library (DEN21)
Lunch will be provided at both locations. Link to the livestreaming for private viewing is also available.
Sign up is mandatory: https://uschsl.co1.qualtrics.com/jfe/form/SV_dd3QgL4sXu5pyYd
Stay tuned for the announcement of upcoming NGS study workshops:
#2 (May 4th)—Analyzing RNA-Seq data with Partek Flow
#3 (May 15th)—Making sense of RNA-Seq data Part 1—Downstream effect analysis (pathways, diseases etc.)
#4 (June 7th)—Making sense of RNA-Seq data Part 2—Upstream regulation analysis (transcription factors etc.)
This workshop is part of the ongoing Bioinformatics Lunch Series, funded by USC Libraries Dean’s Challenge Grant.
Please let us know if you have any questions.
USC Libraries Bioinformatics Service
nmlbio@usc.edu
https://nml.usc.edu/bioinformatics
NGS Workshop #1-- “Key Considerations for NGS Experimental Design”
With a primary focus on RNA-Seq experiments, this workshop covers the following topics:
• Proper number of replicates
• Optimal sequencing depth
• Appropriate read type and length
• Quick points on designing single-cell RNA-Seq, ChIP-Seq, and DNA-Seq experiments
• Find the right sequencing service providers
Time Noon - 1 pm, Wednesday, April 18th
Locations
1. Health Science Campus
West Conference Room, Norris Medical Library
2. University Park Campus (via livestreaming)
Learning Center, Wilson Dental Library (DEN21)
Lunch will be provided at both locations. Link to the livestreaming for private viewing is also available.
Sign up is mandatory: https://uschsl.co1.qualtrics.com/jfe/form/SV_dd3QgL4sXu5pyYd
Stay tuned for the announcement of upcoming NGS study workshops:
#2 (May 4th)—Analyzing RNA-Seq data with Partek Flow
#3 (May 15th)—Making sense of RNA-Seq data Part 1—Downstream effect analysis (pathways, diseases etc.)
#4 (June 7th)—Making sense of RNA-Seq data Part 2—Upstream regulation analysis (transcription factors etc.)
This workshop is part of the ongoing Bioinformatics Lunch Series, funded by USC Libraries Dean’s Challenge Grant.
Please let us know if you have any questions.
USC Libraries Bioinformatics Service
nmlbio@usc.edu
https://nml.usc.edu/bioinformatics
Sunday, March 18, 2018
“R for Bioinformatics” Workshop Series – USC Libraries Bioinformatics
The USC Libraries Bioinformatics Service is pleased to present the “R for Bioinformatics” workshop series. Knowing how to use R is a valuable skillset, as numerous cutting-edge tools for various genomic data analysis are written in R. This workshop series is aimed at training researchers in the varied applications of R for bioinformatics.
The first two hands-on workshops of this series are designed for those with no or little experiences in R but want to achieve basic competency in R usage.
Workshop 1—R and Bioinformatics (4 hr)
• Introduction to R and learning R for bioinformatics
• Using RStudio – an integrated development environment for R
• The general context and concepts of R programming
• Commonly used functions for manipulating bioinformatics data
Workshop 2—Bioconductor and EdgeR (4 hr)
• More commonly used functions for manipulating and visualizing bioinformatics data
• Introduction to bioinformatics package repositories: CRAN and Bioconductor
• Bioinformatics R Packages Case Study 1 - Using EdgeR for Differential Expression analysis.
Before you sign up:
1. Participants are required to attend BOTH workshops.
2. As seating is limited to 10 participants per workshop session, registration is mandatory and must be fulfilled.
3. Participants are required to bring their own laptops.
4. Additional sessions of both workshops may be offered in near future—register to get on the waiting list.
University Park Campus
Workshop 1: 10am to 2pm, Wednesday, March 28th, 2018
Learning Center, Wilson Dental Library (DEN21)
Workshop 2: 10am to 2pm, Friday, April 6th, 2018
Learning Center, Wilson Dental Library (DEN21)
Health Science Campus
Workshop 1: 10am to 2pm, Tuesday, April 3rd, 2018
East Conference Room (Basement Level), Norris Medical Library
Workshop 2: 10am to 2pm, Tuesday, April 10th, 2018
Computer Classroom (2nd Level), Norris Medical Library
Lunch will be provided at all sessions. Sign up with the link below:
https://tinyurl.com/y8cvjj5p
This workshop is part of the ongoing Bioinformatics Lunch Series, funded by USC Libraries Dean’s Challenge Grant.
Please let us know if you have any questions.
Eddie Loh, Yibu Chen, and Meng Li
USC Libraries Bioinformatics Service
nmlbio@usc.edu
https://nml.usc.edu/bioinformatics
The first two hands-on workshops of this series are designed for those with no or little experiences in R but want to achieve basic competency in R usage.
Workshop 1—R and Bioinformatics (4 hr)
• Introduction to R and learning R for bioinformatics
• Using RStudio – an integrated development environment for R
• The general context and concepts of R programming
• Commonly used functions for manipulating bioinformatics data
Workshop 2—Bioconductor and EdgeR (4 hr)
• More commonly used functions for manipulating and visualizing bioinformatics data
• Introduction to bioinformatics package repositories: CRAN and Bioconductor
• Bioinformatics R Packages Case Study 1 - Using EdgeR for Differential Expression analysis.
Before you sign up:
1. Participants are required to attend BOTH workshops.
2. As seating is limited to 10 participants per workshop session, registration is mandatory and must be fulfilled.
3. Participants are required to bring their own laptops.
4. Additional sessions of both workshops may be offered in near future—register to get on the waiting list.
University Park Campus
Workshop 1: 10am to 2pm, Wednesday, March 28th, 2018
Learning Center, Wilson Dental Library (DEN21)
Workshop 2: 10am to 2pm, Friday, April 6th, 2018
Learning Center, Wilson Dental Library (DEN21)
Health Science Campus
Workshop 1: 10am to 2pm, Tuesday, April 3rd, 2018
East Conference Room (Basement Level), Norris Medical Library
Workshop 2: 10am to 2pm, Tuesday, April 10th, 2018
Computer Classroom (2nd Level), Norris Medical Library
Lunch will be provided at all sessions. Sign up with the link below:
https://tinyurl.com/y8cvjj5p
This workshop is part of the ongoing Bioinformatics Lunch Series, funded by USC Libraries Dean’s Challenge Grant.
Please let us know if you have any questions.
Eddie Loh, Yibu Chen, and Meng Li
USC Libraries Bioinformatics Service
nmlbio@usc.edu
https://nml.usc.edu/bioinformatics
Sunday, October 22, 2017
Sunday, October 8, 2017
Ingenuity Pathway and Variants Analysis software Onsite training at USC, Thur Oct. 26, 2017
USC Libraries Bioinformatics Service is pleased to announce the Ingenuity Pathways (IPA) and Ingenuity Variants (IVA) software onsite training at USC. With live demos and hands-on practices, this workshop will help you learn to use the two powerful software to understand the underlying biology of your high-throughput data. See attached flyer for more information.
Time: 9 am to 4:30 pm, Thursday, Oct. 26, 2017
Location: McKibben Annex 249 (MCH), Health Sciences Campus
Breakfast and Lunch will be provided
Registration is mandatory as seating is limited: https://uschsl.co1.qualtrics.com/jfe/form/SV_b8y8l4V8lBO89kp
Training agenda
8:30am: Coffee/snacks provided by USC Libraries
9-noon: Ingenuity Pathway Analysis (IPA) Hands-on Training
12-1pm: Lunch provided by QIAGEN
1-2:00pm: New cutting-edge tools in IPA
• IsoProfiler Enhancements
• Phosphorylation Analysis
• Analysis Match
2:00-4:00pm: Ingenuity Variant Analysis (IVA) Hands-on Training
This workshop is part of the FY2018 USC Libraries Bioinformatics Training Series, funded by USC Libraries Dean’s Challenge Grant.
Please let us know if you have any questions.
USC Libraries Bioinformatics Service
nmlbio@usc.edu
nml.usc.edu/bioinformatics
Time: 9 am to 4:30 pm, Thursday, Oct. 26, 2017
Location: McKibben Annex 249 (MCH), Health Sciences Campus
Breakfast and Lunch will be provided
Registration is mandatory as seating is limited: https://uschsl.co1.qualtrics.com/jfe/form/SV_b8y8l4V8lBO89kp
Training agenda
8:30am: Coffee/snacks provided by USC Libraries
9-noon: Ingenuity Pathway Analysis (IPA) Hands-on Training
12-1pm: Lunch provided by QIAGEN
1-2:00pm: New cutting-edge tools in IPA
• IsoProfiler Enhancements
• Phosphorylation Analysis
• Analysis Match
2:00-4:00pm: Ingenuity Variant Analysis (IVA) Hands-on Training
This workshop is part of the FY2018 USC Libraries Bioinformatics Training Series, funded by USC Libraries Dean’s Challenge Grant.
Please let us know if you have any questions.
USC Libraries Bioinformatics Service
nmlbio@usc.edu
nml.usc.edu/bioinformatics
IPA_IVATrainingOct262017USC by uscbiscgrad on Scribd
Sunday, October 1, 2017
Monday, November 28, 2016
Bioinformatics Specialist Event - 12/7/16
Norris Medical Library Bioinformatics Service is recruiting a new bioinformatics specialist. We cordially invite you to attend the second candidate presentation “ChIP-seq Data Analysis”. This one-hour presentation will introduce the basic principles of analyzing ChIP-seq data. Attendees will learn the fundamentals of ChIP-seq experimental design, data processing and downstream analysis with popular open-source tools on the Galaxy platform (https://usegalaxy.org).
Topics will include:
- Introduction to ChIP-seq
- Quality control on sequencing reads
- Reads alignment to a reference genome
- Data normalization
- ChIP-seq peak calling
- Data visualization with the Integrated Genome Browser
- Functional annotation of ChIP-seq peaks
- Analyzing peaks for transcription factor binding sites
Time: Noon – 1pm, Wednesday, December 7th.
Location: HSC—West Conference Room (basement level), Norris Medical Library
UPC—Live broadcast, Learning Center, Wilson Dental Library
The presentation can also be viewed on your own computer via live broadcast
Lunch will be provided at both in-person locations, seats are limited.
Registration is mandatory: https://uschsl.co1.qualtrics.com/SE/?SID=SV_bxvpsWw21HxJvz7
Monday, November 21, 2016
Bioinformatics Specialist Candidate Presentation #1
Norris Medical Library Bioinformatics Service is recruiting a new bioinformatics specialist. We cordially invite you to attend the first candidate presentation “Identifying Quality Variation in High-Throughput Sequencing Datasets”. This one-hour workshop will focus on identifying sets of variants that can be used for evolutionary and population genetic inference. Attendees will learn the key concepts and steps to call and filter variants from sequencing reads.
The workshop will
- Be applicable to both model and non-model systems
- Cover the data structures of each of the major file formats in high-throughput data analysis (FASTQ, SAM, and VCF)
- Introduce a number of standard analysis tools, including BWA and the Genome Analysis Toolkit (GATK)
- Include suggestions on how to appropriately filter variants
- Illustrate how to perform analyses using the Unix command line and Galaxy
Time: 11 AM – noon, Wednesday, Nov. 30th.
Location: HSC—West Conference Room (basement level), Norris Medical Library
UPC—Live broadcast, Learning Center, Wilson Dental Library
The presentation can also be viewed on your own computer via live broadcast
Lunch will be provided at both in-person locations, seats are limited.
Registration is mandatory: https://uschsl.co1.qualtrics.com/SE/?SID=SV_79TfRpbbpAlkwNT
Wednesday, November 16, 2016
Internship Opportunity In Fitness/Dietary Products
Background & Summary
A Los Angeles-based start-up company that's in the very early stages of developing fitness/dietary products seeks a Genomics/Bioinformatics Intern.
Summary: Work with a personalized genomics fitness start-up company to act as liaison between our fitness professionals and our DNA sequencing lab. Further, the position will develop web applications for visualizing the genetic data.
Requirements
Minimum Education: Presently pursuing a Masters of Science or higher in Genomics, Bioinformatics, Computational Biology or a technical field that requires extensive genomic analysis and computational programming.
Minimum Experience: In-depth understanding of genomics, genetic variation, SNP arrays and the ability to work with our fitness professionals to translate the data into easily understandable analysis for our fitness clients.
Other Requirements: Programming skills also required to convert the sequencing data into web-based reports in an automated and high volume basis. Experience with Perl, R, Java, SQL and/or Python.
Start Date: December 2016.
Next Steps
Interested students can reach out to Douglass Burleson at burleson@usc.edu
Tuesday, August 30, 2016
Should we license CLC Genomics Workbench?
We need your input for making the right decision!
Dear Colleagues,
We invited QIAGEN to give four webinar demos of CLC Genomics Workbench’s features and functionalities, and we need to know if you find this software useful to your research before making a decision on the licensing. Please follow the link below to submit your feedback no later than Sept. 6, 2016:
https://uschsl.co1.qualtrics.com/SE/?SID=SV_29suhYN8MWX77O5
If you were unable to attend the webinar demos, you can watch the recorded sessions via the links below:
Session 1—Introduction and basic molecular manipulation (1hr)
Session 2—RNA-seq analysis (including small RNA) (1hr)
Session 3—DNA-seq analysis and epigenomic (ChIPseq) pipelines (1hr)
Session 4—De novo assembly and Microbial Module (metagenomics) (1.5hr)
Please let us know if you have any questions,
Yibu Chen and Meng Li
Bioinformatics Service Program
Norris Medical Library
University of Southern California
nmlbio@usc.edu
http://nml.usc.edu/bioinformatics
323-442-3309 (Yibu)
323-442-3447 (Meng)
Dear Colleagues,
We invited QIAGEN to give four webinar demos of CLC Genomics Workbench’s features and functionalities, and we need to know if you find this software useful to your research before making a decision on the licensing. Please follow the link below to submit your feedback no later than Sept. 6, 2016:
https://uschsl.co1.qualtrics.com/SE/?SID=SV_29suhYN8MWX77O5
If you were unable to attend the webinar demos, you can watch the recorded sessions via the links below:
Session 1—Introduction and basic molecular manipulation (1hr)
Session 2—RNA-seq analysis (including small RNA) (1hr)
Session 3—DNA-seq analysis and epigenomic (ChIPseq) pipelines (1hr)
Session 4—De novo assembly and Microbial Module (metagenomics) (1.5hr)
Please let us know if you have any questions,
Yibu Chen and Meng Li
Bioinformatics Service Program
Norris Medical Library
University of Southern California
nmlbio@usc.edu
http://nml.usc.edu/bioinformatics
323-442-3309 (Yibu)
323-442-3447 (Meng)
Friday, June 10, 2016
UPC Bioinformatics Day - Workshops and User Event - June 20
As we are getting close to starting a bioinformatics service for the University Park Campus research community, the NML Bioinformatics Service is pleased to present the UPC Bioinformatics Day event on Monday June 20. The event consists of two workshops on RNA-seq experiment design and data analysis AND gene study using powerful literature and data mining tools; as well as a user session over lunch to discuss about your bioinformatics needs and how our service can support your research now and in the future.
UPC Bioinformatics Day Agenda
Time: Monday June 20, 8:30 am to 1 pm
Location: Learning Center, Wilson Dental Library (DEN 21)
Breakfast and lunch are provided for all registered attendees.
8:45 AM Breakfast
9:00 AM—10:30 AM Workshop #1: RNA-seq experiment design and data analysis
Part One--“Key considerations in RNA-seq experimental design”.
Covering some of the most important issues in RNA-seq experiment preparation, we will help you avoid making common and costly mistakes in designing RNA-seq experiments.
Part Two--“Analyze RNA-seq data with Partek Flow”
We will provide an overview on RNA-seq data analysis, with live demo of Partek Flow. It is specifically designed for USC researchers who are planning RNA-seq experiments and/or already have RNA-seq data to be analyzed.
10:40 AM—Noon Workshop #2: Gene study using powerful literature and data mining tools
Part One--“Know more about your genes WITHOUT reading literature”.
We will showcase how you can leverage our bioinformatics tools to dramatically reduce your time spent on literature study while stay better informed and carry out more efficient research on the gene of your interests.
Part Two--“Beyond Literature: Knowledge Discovery with Public Data Mining”.
We will showcase how you can leverage our bioinformatics tools to effectively search for pre-analyzed public datasets and extract relevant information to support/refine your research hypothesis and findings.
Noon—1 PM Lunch session: User needs discussion, Q&A on NML Bioinformatics Service
Please come to our workshops or just join us for the lunch session and let us know your bioinformatics needs and how can we support your research.
Registration is mandatory as the seating for this event is limited to 40 attendees.
https://uschsl.co1.qualtrics.com/SE/?SID=SV_78p9FVQCWVG8aTX
The UPC Bioinformatics Day is funded by USC Libraries Dean’s Challenge Grant.
Please let us know if you have any questions.
Yibu Chen and Meng Li
Bioinformatics Service
Norris Medical Library
University of Southern California
nmlbio@usc.edu
nml.usc.edu/bioinformatics
323-442-3309 (Yibu)
323-442-3447 (Meng)
UPC Bioinformatics Day Agenda
Time: Monday June 20, 8:30 am to 1 pm
Location: Learning Center, Wilson Dental Library (DEN 21)
Breakfast and lunch are provided for all registered attendees.
8:45 AM Breakfast
9:00 AM—10:30 AM Workshop #1: RNA-seq experiment design and data analysis
Part One--“Key considerations in RNA-seq experimental design”.
Covering some of the most important issues in RNA-seq experiment preparation, we will help you avoid making common and costly mistakes in designing RNA-seq experiments.
Part Two--“Analyze RNA-seq data with Partek Flow”
We will provide an overview on RNA-seq data analysis, with live demo of Partek Flow. It is specifically designed for USC researchers who are planning RNA-seq experiments and/or already have RNA-seq data to be analyzed.
Part One--“Know more about your genes WITHOUT reading literature”.
We will showcase how you can leverage our bioinformatics tools to dramatically reduce your time spent on literature study while stay better informed and carry out more efficient research on the gene of your interests.
Part Two--“Beyond Literature: Knowledge Discovery with Public Data Mining”.
We will showcase how you can leverage our bioinformatics tools to effectively search for pre-analyzed public datasets and extract relevant information to support/refine your research hypothesis and findings.
Please come to our workshops or just join us for the lunch session and let us know your bioinformatics needs and how can we support your research.
Registration is mandatory as the seating for this event is limited to 40 attendees.
https://uschsl.co1.qualtrics.com/SE/?SID=SV_78p9FVQCWVG8aTX
The UPC Bioinformatics Day is funded by USC Libraries Dean’s Challenge Grant.
Please let us know if you have any questions.
Yibu Chen and Meng Li
Bioinformatics Service
Norris Medical Library
University of Southern California
nmlbio@usc.edu
nml.usc.edu/bioinformatics
323-442-3309 (Yibu)
323-442-3447 (Meng)
Monday, March 28, 2016
Know more about your genes WITHOUT reading literature
Dear Colleagues,
• Is your research currently focusing on some specific genes?
• Don’t have enough time to read all the literature relevant to your genes?
• Do you know the vast public genomic data could help with your experiment design?
Norris Medical Library Bioinformatics Service is pleased to present “Know more about your genes WITHOUT reading literature”. This one-hour workshop will showcase how you can leverage our bioinformatics tools to dramatically reduce your time spent on literature study while stay better informed and carry out more efficient research on the gene of your interests.
Time Noon—1 pm, Friday, April 8, Lunch will be provided
Location Norris Medical Library, West Conference Room (basement level in the library)
Registration is mandatory as the seating for this workshop is limited to 40 attendees per session:
https://uschsl.co1.qualtrics.com/SE/?SID=SV_0ifR4Gaa3KKtwAR
This workshop is the third installment of the ongoing Bioinformatics Lunch Series, funded by USC Libraries Dean’s Challenge Grant.
Please let us know if you have any questions.
Yibu Chen and Meng Li
Bioinformatics Service
Norris Medical Library
University of Southern California
nmlbio@usc.edu
nml.usc.edu/bioinformatics
323-442-3309 (Yibu)
323-442-3447 (Meng)
• Is your research currently focusing on some specific genes?
• Don’t have enough time to read all the literature relevant to your genes?
• Do you know the vast public genomic data could help with your experiment design?
Norris Medical Library Bioinformatics Service is pleased to present “Know more about your genes WITHOUT reading literature”. This one-hour workshop will showcase how you can leverage our bioinformatics tools to dramatically reduce your time spent on literature study while stay better informed and carry out more efficient research on the gene of your interests.
Time Noon—1 pm, Friday, April 8, Lunch will be provided
Location Norris Medical Library, West Conference Room (basement level in the library)
Registration is mandatory as the seating for this workshop is limited to 40 attendees per session:
https://uschsl.co1.qualtrics.com/SE/?SID=SV_0ifR4Gaa3KKtwAR
This workshop is the third installment of the ongoing Bioinformatics Lunch Series, funded by USC Libraries Dean’s Challenge Grant.
Please let us know if you have any questions.
Yibu Chen and Meng Li
Bioinformatics Service
Norris Medical Library
University of Southern California
nmlbio@usc.edu
nml.usc.edu/bioinformatics
323-442-3309 (Yibu)
323-442-3447 (Meng)
Tuesday, February 9, 2016
Workshop | Introduction to High-Performance Computing at USC
Dear Colleagues:
• Have large data sets such as Next-Generation Sequencing data?
• Need to perform computationally intensive analysis such as NGS data alignment, genome assembly, or protein structure analysis?
Then come and join us to find out how USC High-Performance Computing (HPC), one of fastest academic HPC in the world, can help you to get the job done super-fast.
USC HPC and Norris Medical Library Bioinformatics Service are proud to present the following workshop:
Introduction to High-Performance Computing at USC
Time: 9am-12pm
Date: Thursday, February 18th, 2016
and
Time: 9am-12pm
Date: Wednesdays, March 9th, 2016
Location: Aresty Auditorium at Health Science Campus
Breakfast: Coffee and snacks will be provided
In this introductory workshop, you will learn:
• A tour of USC’s HPC network
• How to apply for a free HPC account with up to 2 TB free disk space
• How to access your HPC account from your own computer
• How to transfer data between your HPC account and your own computer
• Linux commands for basic file/directory manipulation
• Write a demo script and run it on HPC cluster
• Software packages, including bioinformatics software, available to you on the HPC Cluster
For the hands-on practice, a workshop account will be created for anyone who does not have an HPC account, but you must register for the workshop by February 13th for the Feb 18th workshop or Feb. 29th for the March 9th workshop, in order to have an account created for you. Those who already have HPC accounts can register at any time.
Register for the Thursday Feb. 18 workshop:
https://uschsl.co1.qualtrics.com/SE/?SID=SV_01a71mLBA7xE73v
Or the Wednesday March 9 workshop (re-run)
https://uschsl.co1.qualtrics.com/SE/?SID=SV_3UZ3triYoVvFWgl
The following software is required and should be downloaded from USC’s ITS website and installed prior to the workshop. We will spend the first ten minutes on how to configure it and connect. Those who have active HPC accounts should test them prior to attending the workshop.
Mac OS X Users
• XQuartz*: quartz.macosforge.org (*X11 no longer comes pre-installed)
• Fetch: itservices.usc.edu/sftp/fetch-5/
Windows Users
• X-Win32: itservices.usc.edu/unix/xservers
• Filezilla: itservices.usc.edu/sftp/filezilla/
We look forward to seeing you at the workshop.
Erin Shaw
Advanced Cyber Infrastructure-Research & Education Facilitator
USC Center for High-Performance Computing (hpc@usc.edu)
Yibu Chen and Meng Li
Bioinformatics Service Program
Norris Medical Library
University of Southern California
nmlbio@usc.edu
http://nml.usc.edu/bioinformatics/
323-442-3309 (Yibu)
323-442-3447 (Meng)
• Have large data sets such as Next-Generation Sequencing data?
• Need to perform computationally intensive analysis such as NGS data alignment, genome assembly, or protein structure analysis?
Then come and join us to find out how USC High-Performance Computing (HPC), one of fastest academic HPC in the world, can help you to get the job done super-fast.
USC HPC and Norris Medical Library Bioinformatics Service are proud to present the following workshop:
Introduction to High-Performance Computing at USC
Time: 9am-12pm
Date: Thursday, February 18th, 2016
and
Time: 9am-12pm
Date: Wednesdays, March 9th, 2016
Location: Aresty Auditorium at Health Science Campus
Breakfast: Coffee and snacks will be provided
In this introductory workshop, you will learn:
• A tour of USC’s HPC network
• How to apply for a free HPC account with up to 2 TB free disk space
• How to access your HPC account from your own computer
• How to transfer data between your HPC account and your own computer
• Linux commands for basic file/directory manipulation
• Write a demo script and run it on HPC cluster
• Software packages, including bioinformatics software, available to you on the HPC Cluster
For the hands-on practice, a workshop account will be created for anyone who does not have an HPC account, but you must register for the workshop by February 13th for the Feb 18th workshop or Feb. 29th for the March 9th workshop, in order to have an account created for you. Those who already have HPC accounts can register at any time.
Register for the Thursday Feb. 18 workshop:
https://uschsl.co1.qualtrics.com/SE/?SID=SV_01a71mLBA7xE73v
Or the Wednesday March 9 workshop (re-run)
https://uschsl.co1.qualtrics.com/SE/?SID=SV_3UZ3triYoVvFWgl
The following software is required and should be downloaded from USC’s ITS website and installed prior to the workshop. We will spend the first ten minutes on how to configure it and connect. Those who have active HPC accounts should test them prior to attending the workshop.
Mac OS X Users
• XQuartz*: quartz.macosforge.org (*X11 no longer comes pre-installed)
• Fetch: itservices.usc.edu/sftp/fetch-5/
Windows Users
• X-Win32: itservices.usc.edu/unix/xservers
• Filezilla: itservices.usc.edu/sftp/filezilla/
We look forward to seeing you at the workshop.
Erin Shaw
Advanced Cyber Infrastructure-Research & Education Facilitator
USC Center for High-Performance Computing (hpc@usc.edu)
Yibu Chen and Meng Li
Bioinformatics Service Program
Norris Medical Library
University of Southern California
nmlbio@usc.edu
http://nml.usc.edu/bioinformatics/
323-442-3309 (Yibu)
323-442-3447 (Meng)
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