Ingenuity Pathways Analysis online training

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

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

Research and Fellowships Week

Research and Fellowships Week is an annual event hosted by USC’s Academic Honors and Fellowships, the Graduate School and the Office of Postdoctoral Affairs. The goal of the week is to discuss opportunities that support research, graduate study, language learning, teaching and internships within the U.S. and abroad. The sessions are open to students of all academic levels, staff and faculty, attendees participate in interactive panels and workshops to explore USC programs and external post-graduate possibilities.

The following activities are geared towards graduate students: 

Monday, November 4
Fellowships for PhD Students in Health Fields, 12:00-12:50pm, HSC Norris Medical Library, West Conference Room

“The Novelty Moves”: How to Pitch Your Research to Potential Funders….and Beyond, 1:00-1:50pm, Doheny Library (DML) 241

Tuesday, November 5
Fellowships for International PhD Students, 1:00-1:50pm, Doheny Library (DML) 241

USC Advanced PhD Fellowships, 2:00-2:50pm, Doheny Library (DML) 241

Wednesday, November 6
Research with Impact: Data and Bibliometrics, 2:00-2:50pm, Doheny Library (DML) 241

Thursday, November 7
Focus on the NSF Graduate Research Fellowship Program, 1:00-1:50pm, Doheny Library (DML) 241

Friday, November 8
Fulbright U.S. Student Program,11:00-11:50am, Hedco Neurosciences Building (HNB 100)

More information about Research and Fellowships Week is available here: https://ahf.usc.edu/events/rfw/

“2019 R for Bioinformatics" Workshop – USC Libraries Bioinformatics

The USC Libraries Bioinformatics Service is pleased to present the 2019 R for Bioinformatics workshop. Knowing how to use R is a valuable skillset as numerous open access and cutting-edge tools for various genomic data analyses are written in R.  This full-day workshop is aimed at training participants to achieve basic competency in using R for simple bioinformatics tasks, which will form the foundation for other more specialized and advanced R analysis packages. This is a beginner workshop and no prior R knowledge is required.

Topics Covered 
• 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 wrangling bioinformatics data
• Practical examples of wrangling bioinformatics data
• Visualization – creating plots using R
• Bioinformatics Package Repositories: CRAN and Bioconductor

The workshops will be conducted at both UPC and HSC. You will be required to bring your own laptops.

UPC:      9am to 4.30pm, Wednesday, October 30th, 2019
Learning Center, Wilson Dental Library (DEN21) 

HSC:      9am to 4.30pm, Tuesday, November 19th, 2019  
Computer Classroom (2nd Level), Norris Medical Library

Limited to 20 participants per workshop. Due to high demand, please register only if you are sure you would be able to attend. Attendance will be checked and no-shows may be subjected to restriction of future bioinformatics services.

Please register at:
https://usc.qualtrics.com/jfe/form/SV_835wUPfkfMXvY1L

Also, we understand that the demand and popularity of R workshops is extremely high and many of you may not be successful in your registration. We have specially packaged last year’s R workshop into a series of online videos where you can learn the same R workshop contents at your own pace. The videos and training materials are available at https://libguides.usc.edu/c.php?g=913498.

Overcoming Research Anxiety: A Mindful Approach to Literature Review Searching

Presented by Kevin Klipfel, Instructional Design & Assessment Librarian, and Elizabeth Galoozis, Head of Information Literacy

This workshop will discuss psychological strategies for approaching literature reviews, such as adopting a process-oriented “growth” mindset toward research, as well as several practical search techniques that will help you feel confident both getting started with your research and knowing when your literature review is complete. Though this workshop is intended for graduate students, all are welcome.

In-person: Thursday, November 7, 3:30-4:30, Leavey Library 113J: More information and RSVP
Online: Tuesday, November 19, 3:00, 4:00: More information and RSVP

Using Zotero to Organize Your Research

At this workshop, get an introduction to, and hands-on practice using, the free, open-source software Zotero, which can help you organize and cite sources. Zotero is particularly good at capturing web content and for creating group and public "libraries" of sources. Bring a laptop or tablet that you normally use for research.

Presented by Elizabeth Galoozis, Head of Information Literacy, USC Libraries

In-person:
• Tuesday, October 22, 12:00-1:00, Leavey Library 113H: More information and RSVP
• Thursday, November 21, 12:30-1:30, VKC Library B40E - Multi-Media Room: More information and RSVP

Online:
• Tuesday, October 29, 2:00-3:00: More information and RSVP
• Monday, November 18, 3:30-4:30: More information and RSVP

External Fellowship writing workshop for early career PhD students

WiSE is gauging interest for a writing workshop in the late Spring and early Fall for eligible WiSE graduate students interested in applying for one of the upcoming external fellowships e.g. National Science Foundation Graduate Research Fellowship Program and the National Defense Science and Engineering Graduate Fellowship Program.

The workshops are intended to review the application components in depth, help participants brainstorm and write their statements, and facilitate peer and faculty review of the finished materials. The workshops will be designed to accommodate the schedules of participants during each semester.

If you are interested in participating, please fill out this short interest survey by next Wednesday, March 6. A follow-up email will be sent to with more information.

Professional Grant Development Workshop

Master the techniques of writing superior winning proposals

February 11-12, 2019
8:30 a.m.- 4:30 p.m.
To be held at the
University of California
Santa Barbara, CA

Sponsored by the Grant Training Center 

This intensive two-day grant proposal workshop is geared towards those who wish to strengthen their grant writing skills, as well as beginners who wish to acquire and master the techniques of preparing and writing winning proposals to various funding agencies. The focus will be on how to effectively write proposals in times of keen competition and limited resources.

Participants will learn how to:
1. Navigate the world of grant procurement
2. Research and identify potential funding sources
3. Address the guidelines of federal and foundation applications
4. Find foundation and corporate giving for the state of California
5. Understand the new federal guidelines for writing winning grants
6. Know the review process and how to address key points for reviewers
7. Write winning grants that stand out against scores of competing submissions
8. Develop focused and realistic budgets
9. Demonstrate the merits, excellence and innovation of your proposal
10. Package professional grant submissions

Our ultimate goal is for you to walk away with a product specific to your interests, which includes the grant design, abstract and budget.

Register

Questions? For more information visit our website www.granttrainingcenter.com or call: 1-866-704-7268
Workshop Fee: $595.00 (includes a comprehensive directory, electronic workbook, certificate of completion, and continental breakfast)
Rebate of $45.00 per person is given for two or more registrants from the same organization.
*Space is limited, and since this class fills up quickly, it is on a first-come, first-serve basis.*

Can't make it?
Join us January 23, 2019 for an
Online Version of This Workshop

THESIS CENTER INFORMATION SESSIONS

As the thesis and dissertation submission deadline approaches for the Fall 2018 semester, the Graduate School will host two information sessions detailing the thesis submission process next week, on Wednesday, September 26th. The Health Sciences Campus session will take place in Hastings Auditorium at 12:00 pm. The University Park Campus session will take place in GFS 106 at 5:00 pm.

Topics will include important information for both students and advisors, such as:
·         Thesis Center navigation
·         submission deadlines
·         required documentation

There will be an opportunity for questions following the presentation.

PhD Pathways: Career Planning an Preparation, Fall Series

We’re pleased to announce the upcoming Fall 2018 series for the PhD Pathways:  Career Planning and Preparation.  Our first event will take place on September 11 at HSC!  We’re excited to feature events throughout the semester at HSC and UPC. 

As we get closer to Spring, we will be sending out the Spring career series.

Please forward questions or comments to Ashley Brooks at brooksas@usc.edu.

Links to register:

All campus workshops: https://bit.ly/2BpwaAQ
Online CV/Resume Critique: https://bit.ly/2OVEGcQ

   PhD Pathways_Career Series Fall 2018 by uscbiscgrad on Scribd

CET Future Faculty Teaching Institute

The Center for Excellence in Teaching (CET) announces the CET Future Faculty Teaching Institute, a semester-long training program that prepares graduate students, planning to pursue academic careers, with an essential background in pedagogy. Students should be enrolled in doctoral or other terminal degree programs and have some TA or teaching experience. Participants who complete the entire program (a minimum of 12 workshops) will be awarded a teaching excellence certificate and can indicate completion of the institute on their CVs. Schools should encourage their graduate students to sign up.

The CET Future Faculty Teaching Institute comprises a series of 14 hands-on, catered lunch workshops throughout the Fall 2018 semester.

The workshops are designed to provide future faculty:
• Best practices for higher ed course design
• Essential pedagogy for teaching and learning
• Strategies for developing an inclusive learning environment
• Practical techniques to enhance student learning
• Opportunities for collaborative peer review

A sampling of specific workshop topics include:
• Facilitating challenging discussions
• Incorporating strategic questioning
• Enhancing student-instructor and student-student interaction
• Designing for multimedia instruction
• Creating effective assessment practices

Gifts will be raffled off for each session.

Participants may elect to attend either the Monday (12:00-1:00) or Tuesday (12:30-1:30) cohort on the UPC campus (room TBA).

For a list of Monday and Tuesday cohort session meeting dates, and to register for the CET Future Faculty Teaching Institute, visit http://cet.usc.edu/institutes/future-faculty-teaching-institute/

[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

“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 

Thesis Center Information Sessions - Spring Dates & Times

The Graduate School will be hosting Thesis Center information Sessions for students who are submitting their thesis or dissertation this Spring. The sessions will be about 50 minutes long. Advisors and faculty are also welcome and encouraged to attend.

There will be one session on University Park Campus, and one session on Health Sciences Campus:
UPC: Wednesday February 28th, 2018 @ 12:00, in THH 301
HSC: Wednesday March 7th, 2018 @12:00, in MCH 156

Topics will include important information for both students and advisors, such as:
• Thesis Center navigation
• submission deadlines
• required documentation

There will be an opportunity for questions following the presentation. These dates and times will also be listed in myGradSchool for reference.

This week on campus - 10/30-11/5

Monday, October 30 | Graduate Student Professionalization Workshop: Dissertation Research and Writing

Monday, October 30 | OIS Halloween Movie Night

Tuesday, October 31 | Halloween Talk: "Ghost of the Past, Ghosts of the Future"

Tuesday, October 31 | Climate Change: Where Are We and Where Do We Go From Here?

Tuesday, October 31 | International Coffee Hour

Wednesday, November 1 | Benefits Fair at UPC

Wednesday, November 1 | What Matters to Me & Why with Sally Pratt

Wednesday, November 1 | Celebration of Dia de Los Muertos

Thursday, November 2 | Benefits Fair at HSC

Thursday, November 2 | USC/Amgen Seminar: Chris Paszty, Amgen—"Sclerostin: from gene discovery to bone building antibodies"

Thursday, November 2 | Pause for Paws - Visiting Therapy Dogs

Saturday, November 4 | Homecoming 2017

Partek Software Onsite Training at USC, Nov. 8-9 2017

   PartekWorkshop USC Nov2017 Updated by uscbiscgrad on Scribd

Research and Fellowships Week

Academic Honors and Fellowships, The Graduate School and the Office of Postdoctoral Affairs present the 3rd Annual Research and Fellowships Week from November 6-10, 2017!

Are you interested in learning more about research at USC?  Curious to find out how award opportunities like the Fulbright U.S. Student Program or fellowships for PhD students can fund future graduate study or research abroad? A variety of interactive sessions and panels will be offered to help answer these questions and more!  Hear from fellow Trojans, USC Faculty, and Foundation Representatives about how research and competitive fellowships complement one another and help enhance your undergraduate, graduate, and professional career.

Please RSVP here!

Monday, November 6
Sessions located in TCC 227.

Research and Fellowships 101 – 11:00-11:50am
Target Audience: Undergraduates
What is research? What is a fellowship? This presentation will offer an introduction to undergraduate research at USC and explain how research experience can be an asset when applying for competitive fellowships such as the Rhodes Scholarship and Fulbright U.S. Student Program.

Warren Bennis Scholars Program – 12:00-12:50pm 
Target Audience: Freshmen, Sophomores
The Warren Bennis Scholars Program is a two-year, honors leadership development experience for USC undergraduate students from all academic disciplines, who manifest high leadership potential and a passion for serving society. Each year, approximately 20 students are invited to begin the program in the fall semester of their junior year.

Focus on Ford Fellowships – 1:00-1:50pm 
Target Audience: Juniors, Seniors, Early Career PhDs
The Ford Fellowship seeks to increase the diversity of the nation’s college and university faculties by increasing their ethnic and racial diversity. In this session, Dr. Rhacel Salazar Parrenas, USC Professor of Sociology and Gender Studies and Regional Ford Liaison will provide an overview of Ford Foundation opportunities that are available to traditionally underrepresented students.

External Fellowships for PhD Students in the Humanities and Social Sciences – 2:00-2:50pm 
Target Audience: PhDs
A panel of funded PhDs will discuss opportunities and tips.

Tuesday, November 7
Sessions located in TCC 227.

Knight-Hennessy Scholars – 12:00-12:50pm
Target Audience: Undergraduates, Master’s
The Knight-Hennessy Scholars Program provides full funding for graduate study at Stanford University, with the goal of developing a new generation of global leaders.

Focus on the NSF Graduate Research Fellowship Program – 1:00-1:50pm 
Target Audience: Juniors, Seniors, Early Career PhDs
The NSF GRFP recognizes outstanding graduate students in NSF-supported science, technology, engineering, and mathematics disciplines who are pursuing research-based Master’s and doctoral degrees at accredited United States institutions.

USC Stevens Center for Innovation – 2:00-2:50pm 
Target Audience: Postdoctoral Scholars, PhDs, Doctoral, Master’s
Staff will present an introduction to working with USC Stevens and cover university intellectual property policies.

Wednesday, November 8
Sessions located in TCC 302.

Rotary Global Grant – 11:00-11:50am
Target Audience: Undergraduates, Master’s, PhDs
Rotary Global Grants are used to fund graduate level study as well as sustainable, measurable, and needs-based community service projects related to one of six areas of focus.

Boren Scholarship – 12:00-12:50pm 
Target Audience: Undergraduates – U.S. Citizenship Required
The Boren Scholarship provides funding to study less commonly taught languages for at least six months in world regions critical to U.S. interests. Applicants should have an interest in national security and working for the federal government for at least one year after graduation.

Postdoc Funding Opportunities Workshop and Information Session – 1:00-1:50pm 
Target Audience: Postdoctoral Scholars, PhDs
This session will cover postdoc funding opportunities, grant writing techniques, and tips from recent award recipients.

USC Advanced PhD Fellowships – 2:00-2:50pm 
Target Audience: PhDs
The USC Graduate School will discuss competitively awarded fellowships for students who have successfully completed the first year of their PhD program.

Thursday, November 9
Sessions located in TCC 227 or, if noted, Health Sciences Campus NRT 503/504.

Focus on Asia: Research, Intern and Study Abroad – 12:00-12:50pm 
Target Audience: Undergraduates, Master’s
Staff from the East Asian Studies Center and Academic Honors and Fellowships will discuss FLAS, Luce and Schwarzman Scholarships among other funding opportunities to support your studies in Asia.

Fellowships for International PhD Students – 1:00-1:50pm 
Target Audience: International PhDs
Staff from the Graduate School will discuss funding available to international PhD students.

Postdoc Funding Opportunities Workshop and Information Session – 1:00-2:30pm *located in HSC NRT 503/504* 
Target Audience: Postdoctoral Scholars, PhDs
This session will cover postdoc funding opportunities, grant writing techniques, and tips from recent award recipients.

External Fellowship Opportunities for PhDs in Health Fields – 3:00-3:50pm *located in HSC NRT 503/504* 
Target Audience: PhDs
A panel of funded PhDs will discuss opportunities and tips.

Friday, November 10
Sessions located in TCC 302.

Fulbright U.S. Student Program – 11:00-11:50am 
Target Audience: Undergraduates, Master’s, PhDs – U.S. Citizenship Required
The Fulbright U.S. Student Program provides funding to carry out a research project, graduate study or teach English for an academic year in over 140 countries outside of the United States.

Click here to RSVP!

PhD Careers Week

Thesis Center Information Session (HSC) and Thesis Center Office Hours (UPC)

The Graduate School will be hosting a Thesis Center information session for students who are submitting their thesis or dissertation. The session will be about 50 minutes long. Advisors and faculty are welcome and encouraged to attend.

There will be one session on Health Sciences Campus:
• Wednesday June 14th, 2017 @ 12:00 PM, in MCH 256

Next week, I will be holding Thesis Center Office Hours. Office Hours will be held in the Graduate School Conference Room, in STU 301, between 6/14/17 and 6/23/17. Office Hours appointments can be scheduled on the Graduate School website, in the Graduate Events page: http://graduateschool.usc.edu/events/.

If students, advisors, or faculty need one-on-one assistance with submitting to Thesis Center, these sessions will be very helpful for them.

Topics will include important information for both students and advisors, such as:
• Thesis Center navigation
• submission deadlines
• required documentation
• Finalizing publishing information with the USC Digital Library

Please pass this incredibly valuable information along to your students and faculty! There will be an opportunity for questions following the presentation. These dates and times will also be listed in myGradSchool for reference.

Science Communication Workshop

The Science Policy Group at USC is working with Sense About Science to put on a half day, hands-on workshop for all interested in science. It will be led by journalists and science communicators. This is intended to encourage scientists to be involved in outreach and learn how others have done so.

March 24, 2017
1pm-6pm (includes dinner)

RSVP here!

Feel free to direct any questions to me.
Liana