Services

Make the most of your investment in BIOVIA solutions with lab-to-plant process consulting, onsite implementation, expert training and superior support

Learning Paths

Select the desired products and roles to display details about training courses that interest you. Don’t see what you’re looking for? Please e-mail the BIOVIA Training Team.

  • Product:
  • Discoverant
  • Discovery Studio
  • Materials Studio
  • Pipeline Pilot
  • Workbook
  • Roles:
  • Administrator
  • Configuration User
  • Developer
  • Expert User and Designer
  • Observational User
  • Scientist

Introduction to Discovery Studio

This course serves as a comprehensive introduction to the Biovia Discovery Studio software suite. The graphical interface, as well as the use of the various modules and modeling tools available within the software are described. The user will become familiar with the software configuration, running protocols, toolbars, command menus, and preferences. Different molecular displays and visualization modes including the data view, hierarchy view, sequence view, as well as data management storage and retrieval are discussed. The creation of story boards (movies), Active X, and 3D Web GL objects are demonstrated. Hands on exercises are included.

Topics:

  • Modeling Applications Available Within Discovery Studio
  • Discovery Studio Architecture and Configurations
  • User Interface
  • Explorers (Tools, Protocol, Files)
  • Windows: Molecule, Sequence, Sequence Annotation, and Chart
  • Selection and Grouping
  • Working with Proteins
  • Running Protocols
  • Collaboration: Storyboards, ActiveX and NEW: Sharing 3D objects on WebGL enabled browsers
  • Customization: Scripting, Toolbars, Tool Sets, Tools Explorer, Tool Panel

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Products
Discovery Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day - 1 day

Scripting

Discovery Studio provides a client interface for working with a variety of documents and protocols. Occasionally, however, it may be desirable to access specific Discovery Studio functionality programmatically. Perl scripts enable you to perform tasks, such as those listed below, by allowing you to manipulate objects in the application's environment, both at the command line and interactively.

Topics:

  • Automate repetitive tasks
  • Link several tasks or calculations together in sequence
  • Explore calculations that are not available from any of the application's modules
  • Integrate with other software
  • Discussion of Perl scripting language

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Products
Discovery Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day - 1 day

Protein-Protein Docking

This course covers the use of the ZDOCK protein-protein docking software and RDOCK energy rescoring programs available within the Discovery Studio suite. The ZDOCK methodology, as well as algorithms for clustering results are described. Methods for the use of guiding protein-protein docking available within Discovery Studio by filtering residues known experimentally to be involved at the protein-protein interface, as well as excluding those known not to be through blocking are demonstrated.

Topics:

  • The significance, importance, and challenges of performing computational protein-protein docking
  • ZDOCK and analysis
  • Refining the poses of RDOCK

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Products
Discovery Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day - 1 day

Protein Homology Modeling

This course introduces students to the theory of protein homology modeling and the tools available within Discovery Studio. Methods for selecting a protein template structure, aligning the template protein sequence to the target sequence, building the homology model and assessing the quality of the protein structural model within the Discovery Studio framework are described. Methods available for refining the protein model within Discovery Studio are presented. Exercises for students to test their skills are provided.

Topics:

  • Assessing the limitations and assumptions in protein homology modeling
  • Selecting an appropriate protein structural template to create a model
  • Aligning your protein target sequence to a protein template sequence
  • Building a protein homology model using Discovery Studio 2016 tools
  • Analyzing the model in terms of quality, energy and structural features
  • Refining the homology model
  • Using the homology model for further studies, including mutagenesis studies, protein-protein docking, or ligand docking for structure-based drug design

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Products
Discovery Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day - 1 day

Antibody Modeling

This course instructs students in the application of the new Antibody Modeling Cascade available within Discovery Studio 2016. This method provides for automatic generation of a 3D model structure for antibody Fab or Fv regions starting from a set of five antibody structures. This course also provides instruction in the manual modeling and alignment tools for antibody structure, identifying framework templates and antibody loops in addition to the use of the Antibody Modeling Cascade. The use of Proteins 3D to verify the modeled antibody structures will be presented. Exercises for students to follow in modeling antibody examples are provided.

Topics:

  • Introduction to antibodies
  • Fab antibody modeling: Antibody Modeling Cascade, Identify Framework Templates, Model Antibody Framework, and Model Antibody Loops
  • Full length antibody modeling
  • Minimization

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Products
Discovery Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day - 1 day

Simulations

This course focuses on working through the Discovery Studio interfaces: CHARMm, DelPhi, and CDOCKER.

Topics:

  • Energy calculations
  • Manual and automatic atom potential typing
  • Energy minimization
  • Molecular dynamics
  • Constraints
  • Solvation models
  • Trajectory analysis
  • Force field-based docking
  • Electrostatic calculations

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Products
Discovery Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day - 1 day

QM/MM

The course provides an overview of quantum mechanics, molecular mechanics and their combination in QM/MM calculations within Discovery Studio.

Topics:

  • When to use QM/MM methods
  • Overview of density functional theory and its implementation in DMol3
  • Overview of molecular mechanics calculations with CHARMm
  • Considerations for the preparation and setup of QM/MM systems
  • Performing QM/MM calculations in Discovery Studio

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Products
Discovery Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day - 1 day

Pharmacophore Modeling in Discovery Studio

This course provides an introduction to pharmacophore modeling in Discovery Studio. It provides an overview of the diverse applications of these tools in drug discovery and design, and is the foundation for subsequent pharmacophore courses.

Topics:

  • Pharmacophore definition and features
  • Pharmacophore application in drug discovery
  • Ligand-pharmacophore scoring and mapping
  • Ligand perception: Conformation generation and Multi-conformer databases

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Products
Discovery Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day - 1 day

Common Feature Pharmacophone Generation

This course covers the generation of qualitative pharmacophores in Discovery Studio, detailing the automated algorithms (HipHop/HipHopRefine) and the applications of these models in drug discovery and design.

Topics:

  • Creating common feature pharmacophores from active ligand training sets
  • Generating pharmacophore-derived alignments of ligands
  • Using data from inactive ligands to add excluded volumes to pharmacophores to reduce false positives
  • Analysis and application of qualitative pharmacophores

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Products
Discovery Studio

Prerequisites
Pharmacophore Modeling in Discovery Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day

3D QSAR Pharmacophore Generation

This course covers the generation of quantitative pharmacophores in Discovery Studio, detailing the automated algorithms (HypoGen/HypoGenRefine) and the applications of these models in drug discovery and design.

Topics:

  • Creating 3D QSAR pharmacophores from activity data training sets
  • Refining pharmacophores with excluded volumes using data from inactive ligands
  • Analysis and application of quantitative pharmacophore

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Products
Discovery Studio

Prerequisites
Pharmacophore Modeling in Discovery Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day

Receptor-Based Pharmacophores

This course provides an overview of the approaches to deriving pharmacophores from receptor structures and presents their applications in diverse molecular modeling workflows. Students are guided through the steps required to create receptor-based pharmacophore models in Discovery Studio.

Topics:

  • Automated protein-ligand pharmacophore generation
  • Multiple ligands alignment-based pharmacophores
  • Fragment-based pharmacophores for lead optimization
  • Structure-based pharmacophores from interactions maps
  • Validation and analysis of receptor-based pharmacophores

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Products
Discovery Studio

Prerequisites
Pharmacophore Modeling in Discovery Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day

Fragment-Based Drug Design in Discovery Studio

This course covers approaches for successful fragment based lead optimization. Topics include fragment generation, analysis, and identification of fragment scaffolds from ligand libraries; as well as growing, replacing, and placing fragments within a protein target.

Topics:

  • Introduction to Fragment-Based Drug Design
  • Working with fragments and proteins in Discovery Studio: Preparation (Retrosynthetic Combinatorial Analysis Procedure (ReCAP) approach) and Analysis
  • Fragment-based drug design modes: REPLACE, GROW, and PLACE

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Products
Discovery Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day - 1 day

Library Design and Analysis

Ideally, compound libraries used for virtual high throughput screening maximize diversity while optimizing key molecular properties. This course discusses the tools within Discovery Studio used to design, analyze, select subsets, and compare combinatorial libraries.

Topics:

  • Library enumeration (reaction-based and R-group/Markush)
  • Diversity selection and clustering
  • Similarity selection
  • Compound selection optimizing multiple molecular properties simultaneously using Pareto methods
  • Selection of subset libraries to complement and augment existing libraries
  • Comparison of libraries

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Products
Discovery Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day - 1 day

Structure-Based Design - Docking

This course provides an overview of the Discovery Studio tools used for docking small molecules into protein targets. The topics include methods used to prepare proteins and ligands for docking, methods to perform different docking methods, and methods for scoring, analyzing, refining, and filtering docking results.

Topics:

  • Preparation for structure-based design – docking
  • Docking methods
  • Scoring of docking results
  • Analysis, refinement, and filtering tools

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Products
Discovery Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day - 1 day

QSAR

This course is an introduction to the QSAR tools available in Discovery Studio and provides an overview of the various different descriptors that can be calculated within the application. The available QSAR algorithms are described and the main parameters affecting each algorithm are highlighted. Students also receive a comparison of the various techniques.

Topics:

  • Introduction to QSAR
  • Preparing data for QSAR analysis
  • Working with descriptors
  • Calculating and using available descriptors
  • Regression techniques: available methods, advantages, and applicability
  • Modern methods: available methods, advantages, and applicability
  • Example workflow: applying the generated models

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Products
Discovery Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day - 1 day

Hierarchy Maintenance

This course enables BIOVIA Discoverant Administrators and those first learning to create hierarchies to provide support for the most common hierarchy changes, including additions of new nodes and parameters based on existing view structures, and updates or additions to conditions applied by the hierarchy. How to create a Hierarchy-Derived Parameter (HDP) is also covered in this course. This course blends self-paced videos and onsite instructor-led training.

Objectives:

  • Provide an understandable BIOVIA Discoverant overview
  • Add a parameters from a template
  • Create and add parameters to a hierarchy
  • Create nodes to affect parameters
  • Create a Hierarchy-Derived Parameter (HDP)
  • Test hierarchy changes

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Products
Discoverant

Prerequisites
Discoverant Exploration, SQL

Delivery
Self-Paced + Onsite

Level
Beginner

Duration
1 day

Roles
Configuration User

Fundamentals of Hierarchy Development

This course covers all aspects of hierarchy development from design through hierarchy creation. The course walks through each step of the process of hierarchy development from connecting Discoverant to source data systems, to view creation best practices, to configuring BIOVIA Discoverant to use the views to configure a hierarchy. This course blends self-paced videos and onsite instructor-led training.

Objectives:

  • Understand the hierarchy definition tool
  • Create and load a stub hierarchy
  • Describe how data flows from the source system to BIOVIA Discoverant
  • Source and context views in depth
  • Configure a hierarchy
  • Work with overlays and spec limits
  • Configure a stability parameter
  • Use PRIMR as a data source

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Products
Discoverant

Prerequisites
Discoverant Exploration, Hierarchy Maintenance, SQL

Delivery
Self-Paced + Onsite

Level
Intermediate

Roles
Configuration User

BIOVIA PRIMR Development

This course provides both lecture and hands-on exercises surrounding the rules and configuration of BIOVIA PRIMR Book and Page Templates. Basic design concepts, creation of HTML forms, system configuration, and utilization of style sheets and JavaScript are discussed. Students then create and manage BIOVIA PRIMR Book and Page Templates using HTML editors and the BIOVIA PRIMR tools.

Objectives:

  • Identify how BIOVIA PRIMR supports 21 CFR Part 11 compliance and other regulatory initiatives
  • Define the Passport methodology and where BIOVIA PRIMR is placed in this implementation methodology
  • Identify the building blocks of hierarchy development
  • Identify and utilize the two parts of BIOVIA PRIMR: Template Manager and Data Entry
  • Identify and utilize the BIOVIA PRIMR user roles
  • Identify the lifecycle of a BIOVIA PRIMR book; from creation, to data entry, to reconciliation, and to export
  • Identify the typical workflow for each BIOVIA PRIMR role

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Products
Discoverant

Prerequisites
Discoverant Exploration, HTML

Delivery
Onsite, Virtual Classroom

Level
Beginner

Duration
2 days

Roles
Configuration User

System Management

This course provides BIOVIA Discoverant administrators with the knowledge necessary to configure and maintain the BIOVIA Discoverant suite of products. Administrators are shown the BIOVIA Discoverant system architecture, are instructed on the administration of users, and are taken through the process of troubleshooting common issues by monitoring logs and interpreting error messages.

Objectives:

  • Describe the architecture of the BIOVIA Discoverant system and manage the various components in the Windows environment
  • Design a security scheme that includes user authentication mechanisms and role-based access to product features
  • Enforce desired system behavior using configuration settings
  • Leverage system auditing and logging to troubleshoot system issues
  • Diagnose and solve database connectivity issues
  • Perform first-level troubleshooting, determine when to contact BIOVIA Support, and assemble the appropriate information for Support calls

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Products
Discoverant

Prerequisites
Discoverant Exploration

Delivery
Onsite, Virtual Classroom

Level
Beginner

Duration
1 day

Roles
Administrator

Data Visualization

This course teaches you how to design and create visual displays of your data in BIOVIA Discoverant. You will learn how to develop useful visualizations, automate their creation, and share them with your appropriate audience.

Objectives:

  • Identify, define, and prepare the necessary components to create a data visualization
  • Gather and filter data to create a data visualization
  • Create a data visualization
  • Expose data visualizations for communication to appropriate parties
  • Utilize the data visualization process to create a visualization that addresses a simple “need” within your area of responsibility

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Products
Discoverant

Prerequisites
Discoverant Exploration

Delivery
Self-Paced

Level
Beginner

Duration
1/2 day

Roles
Observational User, Expert User and Designer, Configuration User

Process and Product Monitoring

This course teaches you application of the BIOVIA Discoverant quality monitoring techniques that increase process intelligence. You will learn to develop quality monitoring systems using the alerting, automation, and data sharing tools.

Objectives:

  • Identify the terminology and tools used for quality monitoring
  • Gather data for quality monitoring in Discoverant
  • Set up a process monitoring system
  • Set up automation tools to facilitate communication and expose data
  • Conduct ongoing monitoring

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Products
Discoverant

Prerequisites
Discoverant Exploration, Data Visualization

Delivery
Self-Paced

Level
Intermediate

Duration
1 1/2 days

Roles
Observational User, Expert User and Designer, Configuration User

Statistical Applications

This course discusses critical fundamental concepts relevant to statistical application in the pharmaceutical and biological technology fields. Students are guided through the process of determining proper statistics, conducting inferential relationship and difference analyses (e.g., t-test, ANOVA, regression), as well as interpreting BIOVIA Discoverant outputs and writing up results.

Objectives:

  • Identify and comprehend key concepts and terminology of statistical application
  • Combine, organize, and clean data for statistical application
  • Identify, conduct, and interpret descriptive statistics
  • Identify conditions appropriate to draw inferences from statistical results
  • Use difference-based inferential statistics to facilitate scientific decision making
  • Use relationship-based inferential statistics to facilitate scientific decision making
  • Be able to communicate statistical results effectively

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Products
Discoverant

Prerequisites
Discoverant Exploration, Data Visualization

Delivery
Onsite

Level
Advanced

Duration
1 day

Roles
Expert User and Designer

Fundamentals of Investigations

This course introduces students to the proper application of the tools available within BIOVIA Discoverant designed to assist in investigational analysis. Through discussion of use cases and interaction with the software, students begin, or continue, to develop their investigational analysis skills in BIOVIA Discoverant.

Objectives:

  • Determine how to utilize data outside of BIOVIA Discoverant and modify existing data within BIOVIA Discoverant for investigations
  • Identify which statistical analyses and visualizations to use in an investigation given the data
  • Conduct an investigation utilizing various BIOVIA Discoverant tools
  • Report the findings of an investigation to stakeholders
  • Identify the top suspects for investigations and automate their investigation

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Products
Discoverant

Prerequisites
Discoverant Exploration, Data Visualization, Statistical Application

Delivery
Onsite, Virtual Classroom

Level
Advanced

Duration
1/2 day

Roles
Expert User and Designer

Leveraging Phase Data for Analysis

The Leveraging Phase Data for Analysis course addresses BIOVIA Discoverant tools that clean out unwanted noise in continuous data within and between features or compare individual features to groups of similar features. Students can compare chromatographic phases, fermentation profiles with process outcomes, and filtration flux profiles within and between batches.

Objectives:

  • Identify how MPA can be leveraged for continuous data and dynamic processes
  • Identify, gather, visualize, and create phases for continuous data
  • Identify how BIOVIA Discoverant can be used to summarize phase data and compare new batches to defined golden batches
  • Utilize MPA to monitor column performance and generate HETP and asymmetry statistics for monitoring on control charts
  • Analyze complex relationships among continuous parameters to identify underlying principal components and develop new hypotheses

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Products
Discoverant

Prerequisites
Discoverant Exploration, Data Visualization, Statistical Application, Process and Product Monitoring

Delivery
Onsite, Virtual Classroom

Level
Advanced

Duration
1/2 day

Roles
Expert User and Designer

Stability Studies and Monitoring

This course provides users with the purposes and the workflows for conducting their stability-oriented job tasks. In accordance with regulatory guidelines, this course reviews data visualizations, ANCOVA-based point-and-click models for expiration dating analysis, as well as control charts to trend and receive alerts on stability study data.

Objectives:

  • Identify the purpose for stability studies and monitoring at your company
  • Identify, gather, organize, and visualize necessary stability data
  • Apply proper modeling for stability expiration analysis and trend monitoring
  • Develop end-user automation and alerting tools to facilitate communication and expose data

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Products
Discoverant

Prerequisites
Discoverant Exploration, Data Visualization

Delivery
Onsite, Virtual Classroom

Level
Advanced

Duration
1/2 day

Roles
Expert User and Designer

Hierarchy Design

This course introduces the concepts required for defining and designing a new BIOVIA Discoverant Hierarchy. Students are taken through the complete design process, from scoping the hierarchy based on the needs and resources present, to creating documents that capture essential information about the process. Students are also taught how to develop requirements for the hierarchy, capture the necessary parameters, and test the implemented hierarchy. Labs and discussion complement the lecture material so that students complete the course with the essential information for carrying out the hierarchy design process.

Objectives:

  • Create a document outlining the primary objectives for creating the hierarchy
  • Identify the information required to assess a client’s needs with regards to a hierarchy
  • Apply knowledge about BIOVIA Discoverant tools, manufacturing processes, and client needs to create Analytical Goals
  • Identify the information required to map a process and create a document that captures that process
  • Translate Analytical Goals and the corresponding process into a hierarchy
  • Evaluate design changes to the hierarchy during implementation and determine if they impact the Analytical Goals
  • Confirm that the Analytical Goals are met by the implemented hierarchy

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Products
Discoverant

Prerequisites
Data Exploration, Data Visualization, PPM, Stability Studies and Monitoring, Leveraging Phase Data Analysis

Delivery
Onsite

Level
Intermediate

Duration
1 day

Roles
Expert User and Designer

Discoverant Exploration

This course introduces students to the various aspects of BIOVIA Discoverant by defining the terminology, interacting with the environment, and exploring job roles associated with each component in the BIOVIA Discoverant suite of products.

Objectives:

  • Identify barriers to successful data aggregation and analysis in the life science industry
  • Identify and describe relationships among the BIOVIA Discoverant suite of products to produce a software solution that improves process understanding
  • Identify and define the terminology, environment, and capabilities associated with each component in the BIOVIA Discoverant suite of products
  • Identify the job roles associated with each component in the BIOVIA Discoverant suite of products.
  • Define the BIOVIA Discoverant implementation process
  • Identify training offerings based on job roles

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Products
Discoverant

Delivery
Self-Paced

Level
Beginner

Duration
1 hour

Roles
Observational User, Expert User and Designer, Configuration User

AG Manager

This course is for users who are currently able to navigate and use BIOVIA Discoverant at a basic level. The course focuses on how to create and manage Analysis Groups (AGs). Students learn the process for creating an AG, and how to access and utilize the AG Manager. An AG is a manageable subset of data extracted from various source systems that you can use to more effectively analyze data.

Objectives:

  • Identify how AG Manager fits into the BIOVIA Discoverant suite of products
  • Utilize BIOVIA Discoverant terminology
  • Identify the structure and function of a hierarchy
  • Describe how to utilize AGs within BIOVIA Discoverant for gathering and sharing process data
  • View and manage data in Table View
  • Navigate and view batch genealogy in BIOVIA Discoverant

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Products
Discoverant

Prerequisites
Discoverant Exploration

Delivery
Self-Paced

Level
Beginner

Duration
1 hour

Roles
Observational User, Expert User and Designer, Configuration User

HVU Data Entry

Technical users who are currently able to navigate BIOVIA Discoverant at a basic level and are familiar with hierarchy structure and source data may be interested in this course. The focus for the HVU Data Entry course is on how to enter parameter data for a published hierarchy.

Objectives:

  • Access HVU Data Entry
  • Identify data entry best practices
  • Manually enter Parameter Set Names and data for discrete, continuous, and replicate parameters
  • Upload data from a tab-delimited data source
  • Copy and paste data from a spreadsheet

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Products
Discoverant

Prerequisites
Discoverant Exploration

Delivery
Self-Paced

Level
Beginner

Duration
1 hour

Roles
Configuration User

HVU Test Execution

The focus of the HVU Test Execution course is on how to use the Hierarchy Verification Utility (HVU) to publish hierarchies, execute tests, and view test results within Hierarchy Manager. Technical users who are currently able to navigate both BIOVIA Discoverant and Hierarchy Manager at a basic level will benefit from this course.

Objectives:

  • Access Hierarchy Manager
  • Publish a hierarchy for use with HVU
  • Execute HVU for testing a new configuration and for regression testing
  • View and evaluate test results

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Products
Discoverant

Prerequisites
Discoverant Exploration

Delivery
Self-Paced

Level
Beginner

Duration
1 hour

Roles
Developer

Feature Extraction

The BIOVIA Discoverant feature extraction tool helps end users analyze and compare continuous data trends by extracting summarized discrete values from the curves. This course is targeted for users who are currently able to navigate BIOVIA Discoverant at a basic level, create Analysis Groups (AGs) that contain continuous data, and identify the concept of offset groups for continuous data.

Objectives:

  • Identify common use cases to apply the feature extraction tool in process monitoring and investigations
  • Align continuous data for analysis
  • Select the desired area and extract a discrete feature (slope, area under the curve, etc.) from continuous data
  • Save the new feature and view the data in a table

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Products
Discoverant

Prerequisites
Discoverant Exploration

Delivery
Self-Paced

Level
Intermediate

Duration
1 hour

Roles
Expert User and Designer

PRIMR Data Entry

Targeted to BIOVIA PRIMR users with a data entry role who have a basic familiarity with browsers, this course walks students through how to enter data from paper records into the BIOVIA PRIMR data entry tool for use in BIOVIA Discoverant.

Objectives:

  • Create a new data entry Book from Book Templates
  • Create new data entry Pages for a Book
  • Enter data into online forms
  • Correct and reject data entry forms
  • Generate productivity and accuracy reports
  • Import XML data

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Products
Discoverant

Prerequisites
Discoverant Exploration

Delivery
Self-Paced

Level
Beginner

Duration
1 hour

Roles
Configuration User

Introduction to Materials Studio

This workshop provides an introduction to the tools and functionality available in Materials Visualizer, the core modules in the Materials Studio suite of software.

Topics:

  • Materials Studio interface and sketching
  • Builders: polymer, crystal, nano, meso
  • Tools
  • Materials Modeling: multiscale, quantum, MM, meso, Crystal, QSAR
  • Scripting in Materials Studio
  • Using the client-server architecture
  • Problem-solving approaches

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Products
Materials Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day - 1 day

Adsorption Locator

BIOVIA Materials Studio Adsorption Locator helps you to find the most stable adsorption sites for a broad range of materials, including zeolites, carbon nanotubes, silica gel, and activated carbon – to name just a few, by carrying out Monte Carlo searches of the configurational space of the substrate-adsorbate system.

Topics:

  • Theory in Adsorption Locator
  • Computational Tasks in Adsorption Locator
  • Results from Adsorption Locator
  • Scripting
  • Comparison with Sorption

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Products
Materials Studio

Prerequisites
Introduction to Materials Studio

Delivery
Onsite, Virtual Classroom

Duration
2 hours

Amorphous Cell

BIOVIA Materials Studio Amorphous Cell is a comprehensive model building tool for creating a wide range of amorphous materials. The behavior of amorphous materials is critical to products such as plastics, glasses, foods, and chemicals.

Topics:

  • Introduction
  • The Construction Task
  • How It Works
  • The Packing and Confined Layer Tasks
  • Scripting with Amorphous Cell
  • Tips and Case Studies

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Products
Materials Studio

Prerequisites
Introduction to Materials Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day

Blends

BIOVIA Materials Studio Blends is used to predict phase diagrams and interaction parameters for liquid-liquid, polymer-polymer, and polymer-additive mixtures in order to study the structural factors affecting the behavior of blends and formulations.

Topics:

  • Theory in Blends
  • Tasks and Analysis in Blends
  • Phase Diagrams
  • Applications and Limitations

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Products
Materials Studio

Prerequisites
Introduction to Materials Studio

Delivery
Onsite, Virtual Classroom

Duration
2 hours

CASTEP, Introduction

BIOVIA Materials Studio CASTEP is an ab initio quantum mechanical program employing Density Functional Theory (DFT) to simulate the properties of solids, interfaces, and surfaces for a wide range of materials classes such as ceramics, semiconductors, and metals. First principle calculations allow researchers to investigate the nature and origin of the electronic, optical, and structural properties of a system without the need for any experimental input.

Topics:

  • Introduction to Solid-State Theory and Density Functional Theory (DFT)
  • Technical aspects of DFT calculations
  • Computational tasks in CASTEP
  • Chemical reactions with CASTEP: Transition state search
  • Properties calculations in CASTEP

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Products
Materials Studio

Prerequisites
Introduction to Materials Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day

CASTEP, Advanced

The CASTEP advanced course offers detailed introduction to accurate prediction of electronic properties, NMR, STM, phonon spectra, core-level spectra, and optical properties.

Topics:

  • Introduction
  • Electronic Properties: band structure, density of states, electron density difference, wave functions, Fermi surfaces
  • Experimental Properties: NMR, STM, phonons, IR and Raman spectroscopy, optical spectroscopy, core-level spectroscopy, work function

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Products
Materials Studio

Prerequisites
Introduction to Materials Studio, CASTEP, Introduction

Delivery
Onsite, Virtual Classroom

Duration
1/2 day

Conformers

BIOVIA Materials Studio Conformers provides access to a comprehensive collection of conformational searching and analysis techniques to characterize molecular conformation and flexibility, to gain insight into geometric and energetic properties, and to probe geometry-property relationships, which have application in many fields including crystallization, catalysis, and polymer studies.

Topics:

  • Conformers Search Methods: systematic grid scan, random sampling search, Boltzmann jump search
  • Calculation Setting Up and Output: preparing the structure, conformers calculation – filter, output

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Products
Materials Studio

Prerequisites
Introduction to Materials Studio

Delivery
Onsite, Virtual Classroom

Duration
2 hours

DFTB+

BIOVIA Materials Studio DFTB+ is an improved implementation of the Density Functional-based Tight Binding (DFTB) quantum simulation method for the study of electronic properties of materials. DFTB+ offers unique capabilities to study and understand systems containing hundreds of atoms. Problems that took more time or compute power than most researchers have available, such as defects in semi-conductors, and interactions between organic and inorganic surfaces, are now practical to study using DFTB+.

Topics:

  • Introduction to DFTB+
  • Derivation of the DFTB+ Method
  • Computational Tasks in DFTB+
  • Properties Calculation
  • Creating Slater-Koster Parameters with the Parameterization Tool
  • Electron Transport Calculations
  • Case Studies

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Products
Materials Studio

Prerequisites
Introduction to Materials Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day - 1 day

DMol3, Introduction

BIOVIA Materials Studio DMol3 combines computational speed with the accuracy of quantum mechanical methods to predict materials properties reliably and quickly. It can predict processes in gas phase, solution, and solid environments. It is broadly applicable to research problems in chemistry, pharmaceuticals, materials science, and chemical engineering, as well as solid state physics.

Topics:

  • Introduction To Solid State Theory and Density Functional Theory (DFT)
  • Technical Aspects Of DFT Calculations
  • Computational Tasks In DMol3
  • Properties Calculations In DMol3

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Materials Studio

Prerequisites
Introduction to Materials Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day

DMol3, Advanced

The DMol3 advanced course offers detailed introduction to accurate prediction of electronic properties, chemical reactions, IR and Raman spectra, optical properties, and electron transport properties.

Topics:

  • Properties calculations in DMol3: band structure, density of states (DOS), electron densities, electrostatics, molecular orbitals, and atomic populations
  • Experimental Properties: chemical reactions, vibrations and vibration spectroscopy, optical excitations, optical spectroscopy, and electron transport

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Products
Materials Studio

Prerequisites
Introduction to Materials Studio, DMol3, Introduction

Delivery
Onsite, Virtual Classroom

Duration
1/2 day

ForcitePlus

BIOVIA Materials Studio ForcitePlus is an advanced classical molecular mechanics tool that allows fast energy calculations and reliable geometry optimization of molecules and periodic systems. ForcitePlus provides the user with great flexibility, offering a range of forcefields and charging methods.

Topics:

  • Forcefield types
  • Nonbond interactions
  • Forcefield typing and change assignment
  • Computational tasks in Forcite
  • Forcefield analysis
  • Forcefield editing
  • Scripting in Forcite

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Products
Materials Studio

Prerequisites
Introduction to Materials Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day - 1 day

GULP

The General Utility Lattice Program, or BIOVIA Materials Studio GULP, is a classical simulations code for performing a wide range of calculations on 3D periodic solids, 2D surfaces, gas phase clusters, and isolated defects in a bulk material. In particular, GULP has a large number of materials-specific forcefields, such as the shell model for simulating ionic materials.

Topics:

  • Theory in GULP
  • Computational Tasks in GULP
  • Forcefield Fitting
  • Surface Properties
  • Properties Calculation
  • Applications

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Products
Materials Studio

Prerequisites
Introduction to Materials Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day - 1 day

Materials Studio Collection in Pipeline Pilot (MSC in PP)

The BIOVIA Pipeline Pilot Materials Studio is a new software solution that allows access and utilization of Materials Studio's premier modeling capabilities within the Pipeline Pilot™ scientific authoring application. Now you can integrate predictive analytics for materials properties seamlessly into your scientific workflows. This allows for a more streamlined approach to materials discovery and improves productivity so that you can spend more time on innovation and less on costly laboratory experimentation.

Topics:

  • Readers, Writers, Viewer, and Reporting Components
  • Manipulation
  • Property Calculators
  • Quantum Mechanics
  • Classical Simulation
  • Crystallization
  • Using the Materials Toolkit
  • The Pipeline Pilot Connector for Materials Studio
  • Parallel Processing

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Products
Materials Studio

Prerequisites
Introduction to Materials Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day - 1 day

MesoDyn

MesoDyn is a dynamic simulation method for studying the long length and time behavior of complex fluid systems, including polymer melts and blends. MesoDyn takes a coarse-grained description of a complex fluid and performs time-evolution dynamics of the density and potential fields of the system.

Topics:

  • Introduction to Mesoscale Simulations
  • Density Functional Theory in MesoDyn
  • Set Up of MesoDyn Calculations
  • Analysis of MesoDyn Calculations
  • Applications

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Products
Materials Studio

Prerequisites
Introduction to Materials Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day

Mesocite (DPD)

BIOVIA Materials Studio Mesocite is a state-of-the-art coarse-grained simulation module for the study of materials at length scales ranging from nanometers to micrometers and time scale from nanoseconds to microseconds. Such materials pervade industrial research in areas such as composites, coatings, cosmetics, and controlled release. Mesocite can provide structural and dynamic properties of fluids in equilibrium, under shear or in confined geometries.

Topics:

  • Introduction to Mesocite
  • Building Meso-Structures
  • Introduction to Dissipative Particle Dynamics
  • Mesoscale Parameter Generation (DPD)
  • Mesocite DPD Setup
  • Mesocite Task Setup
  • Mesocite Analysis & Scripting

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Products
Materials Studio

Prerequisites
Introduction to Materials Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day

Morphology

BIOVIA Materials Studio Morphology allows you to predict crystal morphology from the atomic structure of a crystal. The application areas include pharmaceuticals, agrochemicals, food sciences, petrochemicals, cements, and commodity and specialty chemicals.

Topics:

  • Theory in Morphology
  • Predicting Morphologies: Bravais-Friedel Donnay-Harker (BFDH) method, growth morphology method, and equilibrium morphology method
  • Crystal Graphs
  • Tasks and Analysis in Morphology
  • Problems in Surface Chemistry

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Products
Materials Studio

Prerequisites
Introduction to Materials Studio

Delivery
Onsite, Virtual Classroom

Duration
2 hours

ONETEP

BIOVIA Materials Studio ONETEP is a linear scaling method, meaning the time required for a calculation increases linearly with the number of atoms. This linear scaling approach is a vast improvement over conventional DFT methods, where the time needed for computation increases at a rate of as much as N3 (where N is the total number of atoms). As a result, the program can be used to model systems larger than possible by using conventional DFT.

Topics:

  • ONETEP Theory
  • Setup of ONETEP Calculations
  • ONETEP Properties and Analysis
  • Case Studies

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Products
Materials Studio

Prerequisites
Introduction to Materials Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day - 1 day

Polymorph

BIOVIA Materials Studio Polymorph is used to predict potential polymorphs of a given compound directly from the molecular structure. It explores and ranks polymorphs of fairly rigid, non-ionic or ionic molecules. The approach is based on the generation of possible packing arrangements in all reasonable space groups to search for the low lying minima in lattice energy.

Topics:

  • Determination of Crystal Structures
  • Theory Behind Polymorph Prediction
  • Setting Up Polymorph Calculations
  • Analyzing the Results
  • Scripting with the Polymorph Module
  • Applications

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Products
Materials Studio

Prerequisites
Introduction to Materials Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day

QMERA

The BIOVIA Materials Studio QMERA module in BIOVIA Materials Studio performs simulations by combining DFT methods from DMol3 and force field methods from GULP. QMERA can be used to model either molecular or periodic systems and can handle hundreds or even thousands of atoms. It is particularly well-suited for modeling problems in chemical reactivity, where an active site is chemically localized. Researchers can use the method to study problems in nanotubes, nanoclusters, and amorphous material.

Topics:

  • Overview of QM/MM
  • The QM/MM Embedding Schemes
  • Handling of the QM/MM Boundary
  • General Consideration for Simulations
  • QMERA Tasks & Analysis
  • QMERA Servers: DMol3 and GULP
  • Applications

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Products
Materials Studio

Prerequisites
Introduction to Materials Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day - 1 day

QSAR

The QSAR module is a comprehensive set of tools for creating statistical regression models between experimental information ('activity') and molecular level characteristics ('descriptors'). The descriptors that can be calculated include a wide range of properties. These can be supplemented by characteristics calculable with other modules: Forcite, VAMP, fast descriptors.

Topics:

  • Introduction to QSAR
  • Initial Data Analysis
  • Descriptors
  • Model Building
  • Genetic Function Approximation
  • Model Validation and Prediction

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Products
Materials Studio

Prerequisites
Introduction to Materials Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day - 1 day

Reflex, Reflex-Plus, X-Cell, and Reflex QPA

BIOVIA Materials Studio Reflex simulates X-ray, neutron, and electron powder diffraction patterns based on models of crystalline materials. Reflex aids the determination of crystal structure, assists the interpretation of diffraction data, and is applied to validate the results of experiment and computation.

Topics:

  • Introduction to Reflex Tools
  • Pattern Processing Tool
  • Powder Indexing Tool
  • Powder Refinement Tool
  • Powder Solve Tool - Separately licensed modules
  • Powder QPA (Quantitative Phase Analysis) Tool - Separately licensed modules
  • Powder Crystallinity Tool

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Products
Materials Studio

Prerequisites
Introduction to Materials Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day - 1 day

Scripting in Materials Studio

This workshop provides an introduction into the Perl-based scripting language that allows access to some of the Visualizer Tools, the Properties Explorer, a range of 3D Atomistic Documents, Study Tables and the Forcite Module (Calculations and Analysis). Students write scripts to draw molecules from scratch; to get information from collection documents, information from trajectory documents, information from study tables; to move molecules (in a zeolite and over a surface), to set up Forcite calculations, and to retrieve selected results along with additional examples.

Topics:

  • Introduction to Scripting in Materials Studio
  • Scripting for Documents
  • Scripting for Tools
  • Scripting for Modules

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Products
Materials Studio

Prerequisites
Introduction to Materials Studio

Delivery
Onsite, Virtual Classroom

Duration
1/2 day - 1 day

Sorption

Molecular adsorption into microporous structures such as zeolites, aluminophosphates, or polymers is crucial in numerous applications including air separation, hydrocarbon cracking, gas sensors, and ion exchange. BIOVIA Materials Studio Sorption provides a means of predicting fundamental properties, such as sorption isotherms (or loading curves) and Henry’s constants, needed for investigating separations phenomena. In addition, modeling can be used to rationalize sorption properties in terms of molecular level processes.

Topics:

  • Fixed Pressure
  • Fixed Loading
  • Henry Constant
  • Adsorption Isotherm
  • Sorbate Location
  • Configuration Sampling: Monte Carlo Methods
  • Other DialogTabs: Energy, Constraints, and Properties
  • Simulation Tips
  • Scripting
  • Adsorption Locator vs. Sorption

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Products
Materials Studio

Prerequisites
Introduction to Materials Studio

Delivery
Onsite, Virtual Classroom

Duration
2 hours

Synthia

BIOVIA Materials Studio Synthia calculates polymer properties using advanced Quantitative Structure-Property Relationships (QSPRs). It allows researchers to rapidly screen candidate polymers for a wide range of properties, and allows the property prediction of copolymer blends.

Topics:

  • Introduction
  • Quantitative Structure Property Relationship (QSPR)
  • Synthia - Connectivity Indices Methods
  • Random Copolymers
  • Simulation Tips

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Products
Materials Studio

Prerequisites
Introduction to Materials Studio

Delivery
Onsite, Virtual Classroom

Duration
2 hours

VAMP

BIOVIA Materials Studio VAMP is a semi-empirical molecular orbital package for molecular organic and inorganic systems. VAMP is an ideal intermediate module between forcefield and first principles methods and is capable of rapidly calculating many physical and chemical molecular properties.

Topics:

  • Theory in VAMP
  • NDDO: MNDO/C, MNDO, AM1, PM3, AM1*, MNDO/d, and PM6
  • ZINDO: CNDO/1, CNDO/2, INDO/1, and INDO/2
  • Calculation Setting Up
  • Properties Calculations and Analysis
  • Case Study: Carbon Nanodots (CNDs): Supramolecular Electron Donor–Acceptor Hybrids Featuring Perylenediimides

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Products
Materials Studio

Prerequisites
Introduction to Materials Studio

Delivery
Onsite, Virtual Classroom

Duration
2 hours

Pipeline Pilot Fundamentals

This introductory course is beneficial for users with little or no Pipeline Pilot experience. The course covers many of the out-of-the-box components. Students are taught how to use these components to modify existing protocols or create new ones. All basic concepts necessary to create or manipulate protocols are covered. Upon completion of the workshop, students will be able to modify existing protocols and create custom protocols utilizing Pipeline Pilot’s wide range of functionality.

Topics:

  • Pipeline Pilot overview
  • Architecture and interface
  • Developing a running protocol
  • Checkpoints and design mode
  • Component collections and types
  • Filters: Control of flow
  • Merge and join
  • Introduction to PilotScript
  • Subprotocols
  • Web Port

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Products
Pipeline Pilot

Delivery
Onsite, Virtual Classroom

Level
Beginner

Duration
1 day

Reporting and Interactive Reporting

This course covers the use of the Pipeline Pilot Reporting Collection. Topics cover the use of the static components, as well as the interactive element components available in the Pipeline Pilot Reporting Collection. Users already familiar with customizing components and developing custom protocols will benefit from this course. On completion of the workshop, students will be able to modify and create reports and input forms for running protocols from a browser utilizing Pipeline Pilot's Reporting Collection.

Topics:

  • Reporting data structure and components
  • Building reports that include: text, images, tables, charts, conditional formatting, interactivity, tooltips, and hyperlinks
  • Creating input forms for running protocols from a browser

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Products
Pipeline Pilot

Prerequisites
Pipeline Pilot Fundamentals

Delivery
Onsite, Virtual Classroom

Level
Intermediate

Duration
1 day

Advanced PilotScript

This course teaches students the more advanced features of PilotScripting, which includes working with arrays and using variables and functions in protocols. Upon completion of the workshop, students should be comfortable with PilotScript and have the ability to use PilotScript to manipulate properties.

Topics:

  • Manipulating property values, lists, and names
  • Conditional statements and loops
  • Working with numbers and strings
  • Local and global variables
  • Anonymous property list functions
  • Debugging
  • String functions and regular expressions
  • Hash tables

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Products
Pipeline Pilot

Prerequisites
Pipeline Pilot Fundamentals

Delivery
Onsite, Virtual Classroom

Level
Intermediate

Duration
1 day

Pipeline Pilot Integration

This course provides students with the knowledge needed to utilize the scripting and 3rd-party integration functionality included in Pipeline Pilot. Topics covered include connecting to databases, RunProgram, SOAP and Web Services, API integration, and optionally VBScript, Perl or Java topics. Upon completion of the workshop, students will be able to modify and create complex components and protocols utilizing Pipeline Pilot’s wide variety of integration capabilities.

Topics:

  • Server-Side Integration
  • Client-Side Integration
  • Databases and ODBC/JDBC
  • Command line components
  • SOAP and Web services
  • Language-based components (VBScript, Perl, Java)
  • Running protocols from the command line
  • Client SDKs (Java, .NET, JavaScript, SOAP)

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Products
Pipeline Pilot

Prerequisites
Pipeline Pilot Fundamentals, Advanced PilotScript

Delivery
Onsite, Virtual Classroom

Level
Advanced

Duration
1/2 day

BIOVIA Foundation Administration

This course is perfect for individuals tasked with the administration of the Pipeline Pilot server and clients. Students learn how to install the server and clients, set up security, share and manage the XMLDB, and more. Upon completion of the workshop, students have the knowledge necessary to successfully set up and administer the Pipeline Pilot server and client.

Topics:

  • Installing and upgrading of BIOVIA Foundation
  • Running the Administration Portal
  • Apache Web Server
  • Setup and configuration
  • Security
  • Managing protocol jobs
  • Backing up, restoring and purging the XMLDB
  • Configuring databases

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Products
Pipeline Pilot

Delivery
Onsite, Virtual Classroom

Level
Intermediate

Duration
1/2 day

Chemistry

This course focuses on various components in the Pipeline Pilot Chemistry Collection. The components are reviewed by examining their parameters and how to use them. Exercises throughout the course demonstrate various uses of the collection such as physical property calculation, library enumeration, clustering, SAR analysis, and MCSS. These functionalities can be used to build protocols; triage screening results; generate, evaluate, and prioritize synthetic targets; and many other useful applications. Upon completion of the workshop, students will be able to modify and create complex protocols utilizing Pipeline Pilot’s wide variety of scientific functionality.

Topics:

  • Calculating molecular properties
  • Manipulating molecules
  • Calculating molecular fingerprints
  • Substructure searching and similarity
  • Enumerating molecules (and create SAR table)
  • Cluster molecules
  • Maximal common substructure

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Products
Pipeline Pilot

Prerequisites
Pipeline Pilot Fundamentals, Advanced PilotScript

Delivery
Onsite, Virtual Classroom

Level
Intermediate

Duration
1 day

Documents and Text

The Pipeline Pilot Documents and Text Collection unifies search, analysis, and reporting of diverse literature sources. This course covers the use of the collection. Upon completion of the workshop, students will have the knowledge necessary to modify and create protocols utilizing the Pipeline Pilot Text Analytics Collection.

Topics:

  • Searching remote databases, and local files and databases
  • Using concept dictionary/ontologies
  • Adding annotation
  • Using natural language processing
  • Applying analytics - correlation/trends
  • Document data modelling
  • Finding chemical names
  • Converting names to structures

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Products
Pipeline Pilot

Prerequisites
Pipeline Pilot Fundamentals, Advanced PilotScript

Delivery
Onsite, Virtual Classroom

Level
Advanced

Duration
1 day

Data Modeling

This course covers both introductory and advanced topics associated with data modeling. This is NOT a statistics course. Students are led through the use of statistics to determine the relationships among their data for the purpose of understanding or prediction.

Topics:

  • Generic Statistics Components
  • Clustering
  • Regression Models
  • Bayesian Models
  • Recursive Partitioning
  • Pareto Optimization
  • Genetic Function Approximation

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Products
Pipeline Pilot

Prerequisites
Pipeline Pilot Fundamentals, Advanced PilotScript

Delivery
Onsite, Virtual Classroom

Level
Advanced

Duration
1 day

R Statistics Components

This course covers the use of the R Statistics Collection for Pipeline Pilot. This is NOT a statistics course. However, students will learn the scope of the R component collection, how the components work, how to process the results, and how to build customized R components. The course is intended for Pipeline Pilot users already familiar with customizing components and developing custom protocols. Upon completion of the workshop, students will have the ability to modify and create complex protocols using the R Statistics component collection.

Topics:

  • Plotting
  • Analysis
  • Clustering
  • Learning
  • Custom R Script

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Products
Pipeline Pilot

Prerequisites
Pipeline Pilot Fundamentals, Advanced PilotScript

Delivery
Onsite, Virtual Classroom

Level
Advanced

Duration
1/2 day

Sequence Analysis

This course covers the use of the Pipeline Pilot Sequence Analysis Collection and is intended for users already familiar with customizing components and developing custom protocols. Upon completion of the workshop, students will have the ability to modify and create complex sequence analysis protocols utilizing Pipeline Pilot’s wide variety of scientific functionality available in the Sequence Analysis Collection.

Topics:

  • Collection Basics
  • Annotations and Features
  • Search and Similarity: alignments, BLAST, HMMs, Entrez, and DAS Utilities
  • Integration Tools: 3rd Party Tools and BioJava
  • Perl & BioPerl

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Products
Pipeline Pilot

Prerequisites
Pipeline Pilot Fundamentals, Advanced PilotScript

Delivery
Onsite, Virtual Classroom

Level
Advanced

Duration
1/2 day

Next Generation Sequencing (NGS) Primer

This course provides a primer in Next Generation Sequencing (NGS) technologies for users who may have a biological background, but are not familiar with NGS. Students learn about current NGS methods in use, the types of data and data files produced by NGS experiments, and scientific questions that can be answered using NGS.

Topics:

  • Molecular Biology Review
  • NGS Overview
  • Sequencing Systems
  • Sequencing Data
  • Types of Sequencing
  • Applications

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Products
Pipeline Pilot

Prerequisites
Pipeline Pilot Fundamentals, Advanced PilotScript, basic understanding of biology

Delivery
Onsite, Virtual Classroom

Level
Advanced

Duration
1/2 day

Basic Next Generation Sequencing (NGS)

This course introduces users to the Next Generation Sequencing (NGS) repository and some of the basic NGS components. The NGS repository serves as the central data and metadata storage hub for NGS experiments, reference sequences, features, variants, and other data types. In addition to learning how to create, manage, and work with their NGS repository, students will be introduced to the NGS collection’s mapping, variant detection, and reporting components.

Topics:

  • Building a Repository
  • Analysis: SNP Detection
  • Viewers
  • Reporting Tools
  • Mapping Components
  • de novo Assembly
  • Variant Detection (including structural variation)
  • Repository Scope
  • Paired End Reads for Illumina
  • Performance

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Products
Pipeline Pilot

Prerequisites
Pipeline Pilot Fundamentals, Advanced PilotScript, Sequence Analysis, basic understanding of NGS technology

Delivery
Onsite, Virtual Classroom

Level
Advanced

Duration
1/2 day

Advanced Next Generation Sequencing (NGS)

This course is a follow-on to the Basic Next Generation Sequencing (NGS) course and builds upon those lessons learned. Topics covered include advanced repository management, performing quality control on reads, extracting data and metadata from the repository, and using the components to analyze ChIP-Seq data. Advanced topics such as performance optimization and file management are also covered.

Topics:

  • Sequence Repository: create, repository tools (rename, delete), and queries
  • RNA-Seq: Cufflinks, Cuffcompare, and Cuffdiff
  • Chip-seq
  • Filters and manipulators
  • de novo Assembly
  • Performance

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Products
Pipeline Pilot

Prerequisites
Pipeline Pilot Fundamentals, Advanced PilotScript, Sequence Analysis, Basic Next Generation Sequencing (NGS), understanding of NGS technology

Delivery
Onsite, Virtual Classroom

Level
Advanced

Duration
1/2 day

Basic Imaging

This course is designed for anyone wanting to use the Pipeline Pilot Imaging Collection. Students learn about data input, structure, manipulations, statistics, and reporting. Hands-on exercises assist students with gaining a firm grasp on the collection.

Topics:

  • Image Processing - Image and pixel manipulation
  • Geometric: rotate, translate, etc.
  • Change image appearance: removing noise, smoothing, improving contrast, etc.
  • Image Analysis, finding objects in images, performing measurements, and classifying objects or images

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Products
Pipeline Pilot

Prerequisites
Pipeline Pilot Fundamentals, Advanced PilotScript

Delivery
Onsite, Virtual Classroom

Level
Advanced

Duration
1/2 day

Image Analysis Basics

This course is designed for non-imaging experts who would like to become familiar with image analysis using comprehensive examples and hands-on exercises. Students learn about sequences and stacks, intensity transformation, spatial filtering, segmentation, machine learning, and more.

Topics:

  • Image channels, sequences and stacks
  • Intensity transformation
  • Spatial filtering
  • Segmentation
  • Learning and clustering

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Products
Pipeline Pilot

Prerequisites
Pipeline Pilot Fundamentals, Advanced PilotScript, Basic Imaging

Delivery
Onsite, Virtual Classroom

Level
Advanced

Duration
1/2 day

Advanced Imaging

This course is designed for imaging experts and takes a deep dive into the advanced features of the Imaging Collection: pixel manipulation, segmentation, object operations, colocalization, machine learning, 3D stacks, BigImage, and more. Hands-on exercises enhance the learning experience.

Topics:

  • Morphology components
  • Math and statistics components
  • Object manipulation components
  • Transforms
  • Learning and clustering components
  • Sequence and stack manipulation components

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Products
Pipeline Pilot

Prerequisites
Pipeline Pilot Fundamentals, Advanced PilotScript, Basic Imaging, Image Analysis Basics

Delivery
Onsite, Virtual Classroom

Level
Advanced

Duration
1 day

Molecular Toolkit

The Molecular toolkit is a software development kit for accessing and modifying molecular data objects in protocols such as atoms, bonds, molecules, reactions and macromolecules. The toolkit is implemented in PilotScript, Perl and Java programming languages and is well suited for extending the native chemistry capabilities of Pipeline Pilot with custom methods. Upon completion of the workshop, students will have the ability to create highly customized components that manipulate molecular objects in Pipeline Pilot.

Topics:

  • Create new molecules
  • Manipulate atoms
  • Manipulate bonds
  • Create new calculable properties

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Products
Pipeline Pilot

Prerequisites
Pipeline Pilot Fundamentals, Advanced PilotScript, Pipeline Pilot Integration, Chemistry

Delivery
Onsite, Virtual Classroom

Level
Advanced

Duration
1/2 day

Plate Data Analytics

The Pipeline Pilot Plate Data Analytics Collection extracts, analyzes, and reports on data from plate-based assays, including but not limited to single measurements, dose-response data, kinetic data, multiplex data, HCS images, and HTS molecules. Upon completion of the workshop students will have the ability to modify and create protocols utilizing the Pipeline Pilot Plate Data Analytics Collection.

Topics:

  • Create custom readers
  • Report and view plate data
  • Combine and split plates
  • Manipulate well properties
  • Create Dilution Series
  • Perform curve fitting
  • Calculate any ECx values
  • Identify hits or outliers
  • Normalize data
  • Calculate plate and well statistics

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Products
Pipeline Pilot

Prerequisites
Pipeline Pilot Fundamentals, Advanced PilotScript

Delivery
Onsite, Virtual Classroom

Level
Advanced

Duration
1/2 day

Pipeline Pilot Self-Paced Training

Pipeline Pilot offers a full suite of self-paced courses. You can purchase the entire suite on a per-user basis, for a one-year duration.

Topics:

  • Pipeline Pilot Fundamentals
  • Pipeline Pilot Administration
  • Pipeline Pilot Cheminformatics
  • Pipeline Pilot Integration
  • Pipeline Pilot PilotScript
  • Pipeline Pilot Reporting

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Products
Pipeline Pilot

Delivery
Self-Paced

Duration
10 hours

Entering Data and Accessing Information

This course is designed for beginning users of BIOVIA Workbook. The content is based on standard workflows used by research scientists. Exercises focus on entering important experimental data into repositories and accessing experimental information that has been stored in the Vault.

Topics:

  • Navigating in Workbook
  • Creating experiments
  • Recording essential experimental information
  • Updating experiments and registering changes
  • Generating reports
  • Searching in Workbook

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Products
Workbook

Delivery
Onsite, Virtual Classroom

Duration
1/2 day - 1 day

Roles
Scientist, Administrator, Developer

Building Forms, Templates, and Tables

This course is designed for advanced users of the BIOVIA Workbook. Students should be familiar with creating new experiments, adding information to experiments, and checking experiments into versioned repositories. Students develop components that can be made available for everyday users to create their own experiments and add essential information to them. Exercises focus on the creation and management of forms, templates, and tables.

Topics:

  • Creating and managing property sets
  • Designing, creating, and managing forms
  • Creating and managing experiment templates
  • Creating table sections within templates
  • Making templates available for use within the Vault
  • Inserting a table section into an experiment template

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Products
Workbook

Prerequisites
Entering Data and Accessing Information

Delivery
Onsite, Virtual Classroom

Duration
1 day

Roles
Administrator, Developer

Workflow Designer

This course teaches students how to develop workflows using Workflow Designer to define a specific process for an experiment. Hands-on exercises help students.

Topics:

  • Workflow Overview
  • Admin elements – signatures, associations, actors – how to create and use them
  • Workflow designer concepts and how they fit together
  • Planning your workflow
  • Stages, transitions, and different types of activities
  • Compiling and publishing a workflow

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Products
Workbook

Prerequisites
Entering Data and Accessing Information

Delivery
Onsite, Virtual Classroom

Duration
1 day

Roles
Administrator

Workbook Administration

This course is for individuals tasked with the administration of Workbook, which includes the development of functions such as groups, users, vocabularies, signature policies, and workflow associations.

Topics:

  • Creating groups and users
  • Assigning permissions
  • Creating repository folders
  • Creating vocabularies and signature policies
  • Configuring applications such as Lookup Service, Registration, and External Repositories
  • Creating workflow associations
  • Transitioning experiment workflow stages

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Products
Workbook

Prerequisites
Entering Data and Accessing Information

Delivery
Onsite, Virtual Classroom

Duration
1/2 day

Roles
Administrator

Application Development and Scripting

This course is designed for programmers with experience using .NET and/or IronPython. Students will gain an understanding of the basics of BIOVIA Workbook and learn how to extend out-of-the-box capabilities. Using the Workbook SDK, students learn about Notebook sections, Notebook Platform API and Symyx Framework API.

Topics:

  • Symyx Framework and Vault: vault objects and properties
  • Workbook Scripting: forms, tables, materials, toolbars, section-level scripting, preparations, text, and file sections
  • Best Practices
  • Scripting using .NET assemblies

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Products
Workbook

Prerequisites
.NET and/or IronPython, Entering Data and Accessing Information; Building Forms, Templates and Tables

Delivery
Onsite

Duration
4 days

Roles
Developer

BIOVIA Workbook Self-Paced Training

BIOVIA offers a self-paced library that comprises 13 modules covering BIOVIA Workbook functionality for end-users. You can purchase access to this library separately, on a per-user basis, for a one-year duration.

Topics:

  • Introduction to Accelrys Electronic Lab Notebook
  • Customize Experiment Lists
  • Create Experiments
  • Add Experimental Information
  • Create a Report
  • Search in Notebook Explorer
  • Work with Section Templates
  • Import Materials
  • Enter Reaction Data
  • Create a Sample Preparation
  • Create a Formulation
  • Work with the Home Page
  • Use the Experiment Workflow

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Products
Workbook

Delivery
Self-Paced

Roles
Scientist

Discoverant Derived Parameters

Targeted for users who are currently able to navigate and use BIOVIA Discoverant at a basic level and who can perform basic Table View functions, this course shows how to use BIOVIA InVision to create new parameters for analysis and reporting.

Objectives:

  • Successfully create a new, derived, discrete parameter using mathematical functions available in BIOVIA InVision
  • Create an empty discrete parameter to be able to manually add new data in BIOVIA InVision
  • Create a new categorical parameter based on a numeric parameter for categorization and analysis

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Products
Discoverant

Delivery
Self-Paced

Roles
Observational User, Expert User and Designer, Configuration User

ODBC for Analysis Groups - External Data Access

This course shows how to use simple SQL queries to pull data from specific Discoverant analysis groups into other applications, such as report writers, business intelligence applications, or statistical analysis engines, using the Open Database Connectivity (ODBC) standard for database connection.

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Products
Discoverant

Delivery
Self-Paced

Roles
Administrator

System Management: Install Video

This video will demonstrate how to install Discoverant and will discuss key points and terms during the installation process. It will also demonstrate execution of Oracle SQL scsripts used by Discoverant.

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Products
Discoverant

Delivery
Self-Paced

Roles
Administrator

Discovery Studio Pipeline Pilot Integration

This course provides a very basic overview of working with Pipeline Pilot components and introduces examples for different levels of DS protocol customization.

Topics:

  • Customize (i.e., promote or de-promote) parameters of existing DS protocols/components
  • Add or remove available components from existing DS protocols/components
  • Create a new component and add to an existing DS protocol
  • Increase automation of DS Protocols (e.g., automate DS protocol to run over all ?les in a speci?c folder)
  • Easily connect to an external relational database
  • Integrate third-party algorithms (e.g., CORINA, proprietary codes for descriptor calculations)

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Products
Discovery Studio, Pipeline Pilot

Delivery
Onsite, Virtual Classroom

Duration
1/2 day - 1 day

Extending BIOVIA Workbook with Pipeline Pilot Protocols

Developed for Protocol developers with Pipeline Pilot experience or those who have completed the Building Pipeline Pilot Protocols class, this class teaches developers to record, organize and secure experimental information to find, share, and reuse critical knowledge globally. Using Pipeline Pilot can greatly increase the functionality of BIOVIA Workbook.

Topics:

  • Integrate Pipeline Pilot into BIOVIA Workbook
  • Allow template builders to extend the functionality of the BIOVIA Workbook with protocols built using all the collections available in Pipeline Pilot
  • Easily connect BIOVIA Workbook menus and buttons to Pipeline Pilot protocols
  • Build an BIOVIA Workbook template
  • Build protocols
  • BIOVIA Workbook components
  • Data exchange conventions
  • Retrieve data using buttons in experiments
  • Analyze tab
  • Configure protocols to run from an experiment
  • Publish and maintain protocols

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Products
Pipeline Pilot, Workbook

Prerequisites
Pipeline Pilot Fundamentals, Advanced PilotScript, BIOVIA Workbook

Delivery
Onsite, Virtual Classroom

Level
Advanced

Duration
1/2 day

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