Workflows & Tools. Data Analysis Review of typical data analyses Reproducibility & provenance Overview of workflows Computer-based scientific.

Module 08

Data AnalysisWorkflows & Tools

Data Analysis

Review of typical data analyses Reproducibility & provenance Overview of workflows Computer-based scientific workflows (SWF) Benefits of SWF Examples of SWF and associated tools

Topics

Data Analysis

After completing this lesson, the participant will be able to: ◦ Understand a subset of typical analyses used◦ Define a workflow◦ Define an SWF◦ Discuss the benefits of workflows in general and SWF in

particular◦ Locate resources for using SWF

Learning Objectives

Data Analysis

Plan

Acquire & Process

AnalyzePreserve

Publish & Share

The Data Life Cycle

Data Analysis

Conducted via personal computer, grid, cloud computing Statistics, model runs, parameter estimations, production of

graphs/plots etc.

Data Analyses

Data Analysis

Processing: subsetting, merging, manipulating◦ Reduction: important for high-resolution datasets◦ Transformation: unit conversions, linear and nonlinear algorithms

Types of Analyses

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Date timeair temp precip

C mm11-Jul-07 5:0027.6 00011-Jul-07 6:0027.6 00011-Jul-07 7:0027.7 00311-Jul-07 8:0028.2 01711-Jul-07 9:0028.5 00011-Jul-07 10:0029.3 00011-Jul-07 11:0030.1 00011-Jul-07 12:0030.4 000

Recreated from Michener & Brunt (2000)

Data Analysis

Graphical analyses◦ Visual exploration of data: search for patterns◦ Quality assurance: outlier detection

Types of Analyses

Box and whisker plot of temperature by monthScatter plot of August Temperatures

Strasser, unpub. data

Data Analysis

Statistical analyses Conventional statistics

-Traditionally apply to experimental data-Examples: ANOVA, MANOVA, linear and nonlinear regression

Types of Analyses

• Rely on assumptions: random sampling, random & normally distributed error,

independent error terms, homogeneous variance

Descriptive statistics• Traditionally apply to observational or

descriptive data• Examples: diversity indices, cluster

analysis, quadrant variance, distance methods, principal component analysis, correspondence analysis

Oksanen 2011

Example of Principle Component Analysis

Data Analysis

Statistical analyses (continued)◦ Temporal analyses: time series◦ Spatial analyses: for spatial autocorrelation◦ Nonparametric approaches: useful when conventional assumptions

violated or underlying distribution unknown◦ Other misc. analyses: risk assessment, generalized linear models, mixed

models, etc. Analyses of very large datasets◦ Data mining & discovery◦ Online data processing

Types of Analyses

Data Analysis

Re-analysis of outputs Final visualizations: charts, graphs, simulations etc.

After Data Analysis

Science is iterative: The process that results in the final product

can be complex

Data Analysis

Reproducibility is at the core of scientific method Complex process = more difficult to reproduce Good documentation required for reproducibility◦Metadata: data about data◦ Process metadata: data about process used to create,

manipulate, and analyze data

Reproducibility

Data Analysis

Process metadata is information about the process used to get to the data outputs

Related concept: data provenance◦Data provenance is information about the origins of data◦Good provenance = able to follow data throughout entire

life cycle (collection, organization & quality control, analyses, visualization)

◦Allows for Replication & reproducibility Analysis for potential defects, errors in logic, statistical errors Evaluation of hypotheses

Process Metadata

Data Analysis

A workflow is a formalization of process metadata Includes precise description of scientific procedure Includes conceptualized series of data ingestion,

transformation, and analytical steps Three components of a workflow:

1. Inputs: Information or material required2. Outputs: Information or material produced & potentially

used as input in other steps3. Transformation rules/algorithms (e.g. analyses)

Overview of Workflows

Data Analysis

Simplest form of workflow: flow chart


Data import into ExcelData import into Excel

Analysis: mean, SDAnalysis: mean, SD

Graph productionGraph production

Quality control & data cleaning


Data Analysis


Workflows in General

Temperature data (T)


Salinity data (S)

Salinity data (S)






“Clean” T & S data“Clean” T & S data

Inputs & Outputs

Summary statisticsSummary statistics

Data in Excel

format

Data in Excel

format

Input: Raw T and S data Output: data in

Excel format

Input: data in Excel format

Data Analysis

Workflows in General



Salinity data (S)

Salinity data (S)






“Clean” T & S data“Clean” T & S data

Transformation Rules

Summary statisticsSummary statistics

Data in Excel

format

Data in Excel

format


Transformation rules describe what is done

to/with the data to obtain the relevant

outputs for publication.

Data Analysis

• Science is becoming more computationally intensive• Most transformations are done via computer programs

• Sharing workflows benefits science• Defining a scientific workflow system makes documenting workflows easier


Data Analysis

A scientific workflow is an “analytical pipeline” Each step can be implemented in different software

systems Each step and its parameters/requirements are

formally recorded This allows reuse of both individual steps and the

overall workflow

Scientific Workflows (SWF)

Data Analysis

Single access point for multiple analyses across software packages

Keeps track of analysis and provenance: enables reproducibility◦ Each step & its parameters/requirements formally recorded

Workflow can be stored Allows sharing and reuse of individual steps or overall

workflow◦ Automate repetitive tasks◦ Use across different disciplines and groups◦ Can run analyses more quickly since not starting from scratch

Benefits of Scientific Workflows (SWF)

Data Analysis

Open-source, free, cross-platform Drag-and-drop interface for workflow construction Steps (analyses, manipulations, etc) in workflow represented

by an “actor” Actors connect via inputs and outputs to form a workflow Possible applications◦ Theoretical models or observational analyses◦ Hierarchical modeling◦ Can have nested workflows◦ Can access data from web-based sources (e.g. databases)

Downloads and more information at kepler-project.org

Example of SWF: Kepler

Data Analysis


Drag & drop components from this list

Actors in workflow

Data Analysis


This model shows the solution to the classic Lotka-Volterra predator prey dynamics model. It uses the Continuous Time domain to solve two coupled differential equations, one that models the predator population and one that models the prey population. The results are plotted as they are calculated showing both population change and a phase diagram of the dynamics.

Data Analysis

Example of SWF: KeplerResulting output

Data Analysis

Open-source Workflow & provenance

management support Geared toward

exploratory computational tasks◦ Can manage evolving SWF◦ Maintains detailed history

about steps & data www.vistrails.org

Other SWF Tools: VisTrails

Screenshot example

Data Analysis

Social networking site to support scientists that use SWF

Allows searching for, sharing, reuse of SWF

Can comment on and discuss contributed SWF

Gateway to journals and data repositories

www.myexperiment.org

Other SWF Tools: myExperiment

Data Analysis

Scientists should document workflows used to create results◦Data provenance◦Analyses and parameters used◦ Connections between analyses via inputs and outputs

Documentation can be informal (for example, a flowchart) or formal (for example, Kepler software)

Best Practices for Data Analysis

Data Analysis

Modern science is computer-intensive◦Heterogeneous data, analyses, software

Reproducibility is important Workflows = process metadata◦Necessary for reproducibility, repeatability, validation

There are formal systems for documenting process metadata◦ Enable storage, sharing, visualization, reuse

Summary

Data Analysis

Gil, Y, E Deelman, M Ellisman, T Fahringer, G Fox, D Gannon, C Goble, M Livny, L Moreau, and J Myers. Examining the Challenges of Scientific Workflows. Computer 40:24–32, 2007.

Michener, K, J Beach, M Jones, B Ludaescher, D Pennington, R Pereira, A Rajasekar, and M Schildhauer. A knowledge environment for the biodiversity and ecological sciences. Journal of Intelligent Information Systems, 29:111–126, August 2007.

Ludäscher, B, I Altintas, S Bowers, J Cummings, T Critchlow, E Deelman, DD Roure, J Freire, C Goble, M Jones, S Klasky, T McPhillips, N. Podhorszki, C Silva, I Taylor, and M Vouk. Scientific Process Automation and Workflow Management. Computational Science Series Ch 13. Chapman & Hall, Boca Raton, 2009.

McPhillips, T, S Bowers, D Zinn, B Ludäscher. Scientific workflow design for mere mortals. Future Generation Computer Systems 25: 541-551, 2009.

B Ludäscher, I Altintas, C Berkley, D Higgins, E Jaeger-Frank, M Jones, E Lee, J Tao, and Y Zhao. Scientific workflow management and the kepler system. Concurrency and Computation: Practice & Experience, 18, 2006.

W Michener and J Brunt, editors. Ecological Data: Design, Management and Processing. Blackwell Science, 180p, 2000.

Resources for Data Analysis & SWF

What did you learn?

START QUIZ

Data Analysis

Analyses

1. A workflow involves the formalization and processing of metadata with a precise description of scientific procedures and analytical steps. Which of the following is a component of a workflow?

The output which is the information produced

The input that contains the information

All of the above

Data Analysis

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Data Analysis

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Data Analysis

Data mining and discovery

2. Which of the following may not be typically used when analyzing a large amount of data?

Grid computing

Pattern searching and decision trees

Spatial analyses

Data Analysis

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Data Analysis


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Data Analysis

Scatter plots

3. After data analysis, outputs can be generated as _______________ .

Box-and-whisker plots

Plots that show you potential data errors

All graphical formats and analyses

Data Analysis

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Data Analysis


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Data Analysis

Reproducibility

4. Best practices for data analysis should involve the documentation of workflows to show results of data provenance, analyses, and parameters used. Workflows are necessary for which of the following?

Repeatability

Validation

All of the above

Data Analysis

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Data Analysis


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Data Analysis

Scientific workflow

5. SWF stands for _________ and offers computer-based formal systems for documenting the metadata process.

Systematic workflow

Scientific workforce

Systematic work information

Data Analysis

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Data Analysis


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Data Analysis

Each step can be implemented in different software systems with requirements formally recorded

6. Which of the following is a key benefit of SFW?

Single access point for multiple analyses.

Workflow can be stored

Allows sharing of individual steps.

All of the above.

Data Analysis

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Data Analysis


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Data Analysis

Good organization

7. ___________ enables one to follow data throughout the entire data life cycle (collection, organization, quality control, analyses, and visualization).

Good data maintenance

Good provenance

Good metadata

Data Analysis

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Data Analysis

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Data Analysis

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Workflows & Tools. Data Analysis Review of typical data analyses Reproducibility & provenance Overview of workflows Computer-based scientific.

Documents

data slide

data analysis slide

data analysis reproducibility

data analysis processing

data analysis process

data process metadata

descriptive data examples

experimental data examples