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University of Cambridge Training

All-provider course timetable

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Mon 16 Jul 2018 – Wed 18 Jul 2018

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Monday 16 July 2018

09:30
Variant Discovery with GATK4 (1 of 4) Finished 09:30 - 16:30 Bioinformatics Training Room, Craik-Marshall Building

This workshop will focus on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. You will learn why each step is essential to the variant discovery process, what are the operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset.

In the course of this workshop, we highlight key functionalities such as the germline GVCF workflow for joint variant discovery in cohorts, somatic variant discovery using MuTect2, and copy number variation discovery using GATK-CNV. All analyses are demonstrated using GATK version 4. Finally, we demonstrate the use of pipelining tools to assemble and execute GATK workflows.

The workshop covers basic genomics, all currently supported Best Practices pipelines as well as pipelining with WDL/Cromwell/FireCloud. This includes the logic of the major pipelines, file formats and data transformations involved, and hands-on operation of the tools using goal-oriented exercises.

  • Day 1: Introduction to Genomics, GATK Best Practices and Pipelining
  • Day 2: Germline short variant discovery (SNPs + Indels)
  • Day 3: Somatic variant discovery (SNVs + Indels + CNVs)
  • Day 4: Writing pipelines with WDL and running them in FireCloud

Please note that this workshop is focused on human data analysis. The majority of the materials presented does apply equally to non-human data, and we will address some questions regarding adaptations that are needed for analysis of non-human data, but we will not go into much detail on those points.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register Interest by linking here.

13:00
Spanish: Beginner Intensive (7 of 9) Finished 13:00 - 15:00 Department of Engineering, CLIC 1

Fun introductory course to Spanish. This course is for those with little or no previous knowledge of Spanish. Communicative context, with videos, audio, texts and conversation.

14:00
Amicus Yellow Box Searching Workshop new CANCELLED 14:00 - 15:00 Cambridge University Development and Alumni Relations, Training Room Suite 2

This session is a working session to help you use yellow box searching for your own data requests. We will cover:

  • Creating a search
  • Checking the results
  • Saving the search

Tuesday 17 July 2018

09:00
Advanced OpenMP new (1 of 6) Finished 09:00 - 13:00 Phoenix Teaching Room 1, New Museums Site
  • Please note that although this course is being hosted at Cambridge, it is being organised and run by EPCC at the University of Edinburgh.
  • OpenMP is the industry standard for shared-memory programming, which enables serial programs to be parallelised using compiler directives.
  • This 3-day course will cover topics including nested parallelism, OpenMP tasks, the OpenMP memory model, performance tuning, hybrid OpenMP + MPI, OpenMP implementations, and new features in OpenMP 4.0/4.5. Hands-on practical programming exercises make up a significant, and integral, part of this course.
  • Access will be given to appropriate hardware for all the exercises, although many of them can also be performed on a standard Linux laptop.
  • To book a place on this course please complete their online registration form which can be found here along with a full description of the course.
09:30
Leading Your Team Through Change (2 of 2) Finished 09:30 - 12:30 Greenwich House, Edmonton Room


Change is a constant feature in today’s workplace and yet many of us find it hard to navigate successfully through change.

Studies show that the line manager has a critical role to play in ensuring staff are ready for change and in successfully implementing it. These sessions will equip you with the skills and attitudes you need to guide, support and motivate your team through the process of change.

Case studies, discussion and activities will provide the opportunity to share ideas and embed skills.

GL Part 2: Reporting in the General Ledger (1 of 2) Finished 09:30 - 13:00 Finance Division, Greenwich House, Ferrara Room (IT Training Room)

This course provides users the opportunity to run General Ledger reports and how to interpret them when managing departmental funds.

You are invited to bring with you any reference documents that you may have detailing your own departmental codes.

Variant Discovery with GATK4 (2 of 4) Finished 09:30 - 16:30 Bioinformatics Training Room, Craik-Marshall Building

This workshop will focus on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. You will learn why each step is essential to the variant discovery process, what are the operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset.

In the course of this workshop, we highlight key functionalities such as the germline GVCF workflow for joint variant discovery in cohorts, somatic variant discovery using MuTect2, and copy number variation discovery using GATK-CNV. All analyses are demonstrated using GATK version 4. Finally, we demonstrate the use of pipelining tools to assemble and execute GATK workflows.

The workshop covers basic genomics, all currently supported Best Practices pipelines as well as pipelining with WDL/Cromwell/FireCloud. This includes the logic of the major pipelines, file formats and data transformations involved, and hands-on operation of the tools using goal-oriented exercises.

  • Day 1: Introduction to Genomics, GATK Best Practices and Pipelining
  • Day 2: Germline short variant discovery (SNPs + Indels)
  • Day 3: Somatic variant discovery (SNVs + Indels + CNVs)
  • Day 4: Writing pipelines with WDL and running them in FireCloud

Please note that this workshop is focused on human data analysis. The majority of the materials presented does apply equally to non-human data, and we will address some questions regarding adaptations that are needed for analysis of non-human data, but we will not go into much detail on those points.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register Interest by linking here.

UTBS: New Provider Training Administrator Training Finished 09:30 - 13:00 University Information Services, Roger Needham Building, Ely Training Room 2

This course is designed for Training Administrators of a new provider on the University Training Booking System (UTBS) and it will take them through theory and practicals on how to administer their training programme on the UTBS.

An interactive workshop, focusing on providing service for both internal (colleagues) and external (readers) customers.

Web Recruitment Training - managing vacancies & sending correspondence Finished 09:30 - 13:00 University Information Services, Roger Needham Building, Ely Training Room 1

This course covers viewing, processing and recording data for applications, adding notes and attachments, generating rejection emails, generating electronic reference requests, processing applicants through the selection process and transferring successful applicants to CHRIS.

10:00
Medicine: The "Big Four" Databases For Your Literature Search Finished 10:00 - 12:00 Clinical School, Medical Library, Library Training Room

One session - four medicine and life science databases - widest coverage for your literature search. PubMed is great, but it doesn't cover all the journals relevant to life sciences and medicine. Embase, Web of Science and Scopus can also be relevant and each covers unique material. Come to this hands-on session to learn how to get the best from each of these "4 tops".

10:30

Bespoke session for Finance team to assist in setting their vision and challenge statements

13:00
Spanish: Beginner Intensive (8 of 9) Finished 13:00 - 15:00 Department of Engineering, CLIC 1

Fun introductory course to Spanish. This course is for those with little or no previous knowledge of Spanish. Communicative context, with videos, audio, texts and conversation.

13:30

An interactive workshop, focusing on providing service for both internal (colleagues) and external (readers) customers.

14:00
GL Part 2: Reporting in the General Ledger (2 of 2) Finished 14:00 - 16:00 Finance Division, Greenwich House, Ferrara Room (IT Training Room)

This course provides users the opportunity to run General Ledger reports and how to interpret them when managing departmental funds.

You are invited to bring with you any reference documents that you may have detailing your own departmental codes.

To provide an opportunity for someone from elsewhere in Finance Division to spend half a day in the Financial Reporting Team to get an overview and appreciation of what they do.

Advanced OpenMP new (2 of 6) Finished 14:00 - 17:00 Phoenix Teaching Room 1, New Museums Site
  • Please note that although this course is being hosted at Cambridge, it is being organised and run by EPCC at the University of Edinburgh.
  • OpenMP is the industry standard for shared-memory programming, which enables serial programs to be parallelised using compiler directives.
  • This 3-day course will cover topics including nested parallelism, OpenMP tasks, the OpenMP memory model, performance tuning, hybrid OpenMP + MPI, OpenMP implementations, and new features in OpenMP 4.0/4.5. Hands-on practical programming exercises make up a significant, and integral, part of this course.
  • Access will be given to appropriate hardware for all the exercises, although many of them can also be performed on a standard Linux laptop.
  • To book a place on this course please complete their online registration form which can be found here along with a full description of the course.

Wednesday 18 July 2018

09:00
Asbestos Awareness Training charged Finished 09:00 - 12:30 Greenwich House, Heidelberg Room

This training will provide delegates with a basic knowledge of asbestos awareness, the risks and the legal requirements under the Control of Asbestos Regulations 2012.

Advanced OpenMP new (3 of 6) Finished 09:00 - 13:00 Phoenix Teaching Room 1, New Museums Site
  • Please note that although this course is being hosted at Cambridge, it is being organised and run by EPCC at the University of Edinburgh.
  • OpenMP is the industry standard for shared-memory programming, which enables serial programs to be parallelised using compiler directives.
  • This 3-day course will cover topics including nested parallelism, OpenMP tasks, the OpenMP memory model, performance tuning, hybrid OpenMP + MPI, OpenMP implementations, and new features in OpenMP 4.0/4.5. Hands-on practical programming exercises make up a significant, and integral, part of this course.
  • Access will be given to appropriate hardware for all the exercises, although many of them can also be performed on a standard Linux laptop.
  • To book a place on this course please complete their online registration form which can be found here along with a full description of the course.
09:15
Communication Skills Introduction: "Are you receiving me?" Finished 09:15 - 15:45 Greenwich House, Edmonton Room


Increase your confidence and skills in one-to-one communication with this highly participative course. Effective communication starts in your head and it isn’t just about the words you say. Your tone of voice, facial expression and body language all communicate a message. This course will help you get your message across more clearly. You will also have the opportunity to practise communication skills on a one-to-one basis.

09:30
Adobe InDesign CC: Introduction to Desktop Publishing Finished 09:30 - 13:00 Phoenix Teaching Room 2, New Museums Site
  • Adobe InDesign CC is the industry leading page design and layout application. You will build up a publication from ready-prepared text, images and graphics in the same way as QuarkXpress and PageMaker.
AR Part 2: Adjustments and Set Up in Accounts Receivable Finished 09:30 - 12:30 Finance Division, Greenwich House, Ferrara Room (IT Training Room)

This course covers the essentials for keeping your AR accounts in order. In addition to showing you how to make corrections, receipt foreign currencies and the required month/year-end reports we will also show you how you can save time by setting up memo lines, sales persons and receivable activities for your department.

Lifting and Manual Handling Finished 09:30 - 11:00 Greenwich House, Kyoto Room

This training is for all staff who are regularly involved in moving and carrying loads and setting up equipment etc. The course involves theory, practical and video. It requires active participation by all attending. The training also includes a practical demonstration of safe lifting and shows a range of lifting aids that are available.

Variant Discovery with GATK4 (3 of 4) Finished 09:30 - 16:30 Bioinformatics Training Room, Craik-Marshall Building

This workshop will focus on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. You will learn why each step is essential to the variant discovery process, what are the operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset.

In the course of this workshop, we highlight key functionalities such as the germline GVCF workflow for joint variant discovery in cohorts, somatic variant discovery using MuTect2, and copy number variation discovery using GATK-CNV. All analyses are demonstrated using GATK version 4. Finally, we demonstrate the use of pipelining tools to assemble and execute GATK workflows.

The workshop covers basic genomics, all currently supported Best Practices pipelines as well as pipelining with WDL/Cromwell/FireCloud. This includes the logic of the major pipelines, file formats and data transformations involved, and hands-on operation of the tools using goal-oriented exercises.

  • Day 1: Introduction to Genomics, GATK Best Practices and Pipelining
  • Day 2: Germline short variant discovery (SNPs + Indels)
  • Day 3: Somatic variant discovery (SNVs + Indels + CNVs)
  • Day 4: Writing pipelines with WDL and running them in FireCloud

Please note that this workshop is focused on human data analysis. The majority of the materials presented does apply equally to non-human data, and we will address some questions regarding adaptations that are needed for analysis of non-human data, but we will not go into much detail on those points.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to Book or register Interest by linking here.

Risk Assessment Finished 09:30 - 12:30 Greenwich House, Minsk Room

The course is designed to give attendees the necessary skills to carry out risk assessments.

Leadership Essentials Finished 09:30 - 16:00 Greenwich House, Jaffna Room


Leadership Essentials is a key programme suitable for all managers, which aims to help them refresh and build their skills and experience in managing others. As well as clarifying key responsibilities, it focuses on critical areas that managers can find more difficult, such as giving and receiving feedback effectively and handling challenging conversations. It incorporates tutor input, opportunities for discussion, reflection and sharing of good practice with other managers.

Before attending, please take some time to review the short films of other University colleagues talking about their role as a manager, Leadership Essentials: Management Responsibilities

Postdocs: Writing a Grant Application with Impact Finished 09:30 - 12:30 Postdoc Centre@ Mill Lane, Eastwood Room

Do you know how to write a successful research grant application? This course is designed for postdocs with little or no experience of getting their research funded. It will explore the current research environment and impact agenda and help you understand how research is funded. You will also experience the process of reviewing applications and gain valuable and timely knowledge about how to get research funded.


Outcomes:

  • Learn tips and strategies to help you to get your current & future projects funded
  • Understand how proposals are assessed by funders
  • Gain experience of reviewing funding applications
  • Gain information about translational research funding and support available to post-docs


Feedback:

“Both the online resources presented, and the focused training sessions were well structured and passed through the importance of well-structured proposal, and often overlooked issues such as impact.”

“[I liked] seeing a grant from another discipline, to realise that a well-written grant (even if not perfect) can be understood also by people external to the field.”

10:30

An overview of the changes to the Cambridge University Libraries Staff Review and Development Process

11:15
Green Labs Cold Storage new Finished 11:15 - 12:15 Clinical School, Addenbrookes, Bay 13, Room A (No Longer in Use)

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13:30
Asbestos Awareness Training charged Finished 13:30 - 17:00 Greenwich House, Heidelberg Room

This training will provide delegates with a basic knowledge of asbestos awareness, the risks and the legal requirements under the Control of Asbestos Regulations 2012.

14:00
Advanced OpenMP new (4 of 6) Finished 14:00 - 17:00 Phoenix Teaching Room 1, New Museums Site
  • Please note that although this course is being hosted at Cambridge, it is being organised and run by EPCC at the University of Edinburgh.
  • OpenMP is the industry standard for shared-memory programming, which enables serial programs to be parallelised using compiler directives.
  • This 3-day course will cover topics including nested parallelism, OpenMP tasks, the OpenMP memory model, performance tuning, hybrid OpenMP + MPI, OpenMP implementations, and new features in OpenMP 4.0/4.5. Hands-on practical programming exercises make up a significant, and integral, part of this course.
  • Access will be given to appropriate hardware for all the exercises, although many of them can also be performed on a standard Linux laptop.
  • To book a place on this course please complete their online registration form which can be found here along with a full description of the course.

A briefing on the SRD process and how to get the most of it

Launch of LinkedIn Learning for the IT Community new Finished 14:00 - 15:00 University Information Services, Roger Needham Building, Norwich Auditorium
  • University Information Services (UIS) invites all University IT staff to celebrate the launch of LinkedIn Learning for the IT Community. View a whistle stop tour of the product, discover the benefits, hear user stories from the IT community and indulge in a celebratory cake.
  • LinkedIn Learning is an online eLearning resource which provides expert led courses developed by industry experts using Lynda.com content, topics include:
- Cloud Computing
- Software Development (C++, Java, PHP, Python, etc.)
- Cybersecurity
- Leadership and Management
- Network and Systems Administration
- Design and Creative Themes
- Data Science
- ITIL and IT Help Desk
- Project Management
- Web Design and Development
Physics Health and Safety - Maxwell Centre Induction new (1 of 2) Finished 14:00 - 14:25 Department of Physics, Maxwell Centre, JJ Thomson Seminar Room (Floor 2)

This induction is required for anyone planning to work unsupervised at the Maxwell Centre, Department of Physics.

It has two parts:

  • Part 1 is for people working anywhere in the building
  • Part 2 is only for those working at the Maxwell laboratories
14:25
Physics Health and Safety - Maxwell Centre Induction new (2 of 2) Finished 14:25 - 14:55 Department of Physics, Maxwell Centre, JJ Thomson Seminar Room (Floor 2)

This induction is required for anyone planning to work unsupervised at the Maxwell Centre, Department of Physics.

It has two parts:

  • Part 1 is for people working anywhere in the building
  • Part 2 is only for those working at the Maxwell laboratories