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28 views52 pages

Python For Bioinformatics 2nd Edition Sebastian Bassi Instant Download

The document provides information about the second edition of 'Python for Bioinformatics' by Sebastian Bassi, including details on its publication, ISBN, and content structure. It is part of the Chapman & Hall/CRC Mathematical and Computational Biology Series, aimed at integrating mathematical and computational methods into biology. Additionally, it includes links to related bioinformatics and programming resources and textbooks.

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Python for Bioinformatics 2nd Edition Sebastian Bassi
Digital Instant Download
Author(s): Sebastian Bassi
ISBN(s): 9781138035263, 1138035262
Edition: 2nd
File Details: PDF, 4.97 MB
Year: 2017
Language: english
PYTHON FOR
BIOINFORMATICS
SECOND EDITION
CHAPMAN & HALL/CRC
Mathematical and Computational Biology Series

Aims and scope:


This series aims to capture new developments and summarize what is known
over the entire spectrum of mathematical and computational biology and
medicine. It seeks to encourage the integration of mathematical, statistical,
and computational methods into biology by publishing a broad range of
textbooks, reference works, and handbooks. The titles included in the
series are meant to appeal to students, researchers, and professionals in the
mathematical, statistical and computational sciences, fundamental biology
and bioengineering, as well as interdisciplinary researchers involved in the
field. The inclusion of concrete examples and applications, and programming
techniques and examples, is highly encouraged.

Series Editors

N. F. Britton
Department of Mathematical Sciences
University of Bath

Xihong Lin
Department of Biostatistics
Harvard University

Nicola Mulder
University of Cape Town
South Africa

Maria Victoria Schneider


European Bioinformatics Institute

Mona Singh
Department of Computer Science
Princeton University

Anna Tramontano
Department of Physics
University of Rome La Sapienza

Proposals for the series should be submitted to one of the series editors above or directly to:
CRC Press, Taylor & Francis Group
3 Park Square, Milton Park
Abingdon, Oxfordshire OX14 4RN
UK
Published Titles
An Introduction to Systems Biology: Statistical Methods for QTL Mapping
Design Principles of Biological Circuits Zehua Chen
Uri Alon An Introduction to Physical Oncology:
Glycome Informatics: Methods and How Mechanistic Mathematical
Applications Modeling Can Improve Cancer Therapy
Kiyoko F. Aoki-Kinoshita Outcomes
Computational Systems Biology of Vittorio Cristini, Eugene J. Koay,
Cancer and Zhihui Wang
Emmanuel Barillot, Laurence Calzone, Normal Mode Analysis: Theory and
Philippe Hupé, Jean-Philippe Vert, and Applications to Biological and Chemical
Andrei Zinovyev Systems
Python for Bioinformatics, Second Edition Qiang Cui and Ivet Bahar
Sebastian Bassi Kinetic Modelling in Systems Biology
Quantitative Biology: From Molecular to Oleg Demin and Igor Goryanin
Cellular Systems Data Analysis Tools for DNA Microarrays
Sebastian Bassi Sorin Draghici
Methods in Medical Informatics: Statistics and Data Analysis for
Fundamentals of Healthcare Microarrays Using R and Bioconductor,
Programming in Perl, Python, and Ruby Second Edition
Jules J. Berman Sorin Drăghici
Chromatin: Structure, Dynamics, Computational Neuroscience:
Regulation A Comprehensive Approach
Ralf Blossey Jianfeng Feng
Computational Biology: A Statistical Biological Sequence Analysis Using
Mechanics Perspective the SeqAn C++ Library
Ralf Blossey Andreas Gogol-Döring and Knut Reinert
Game-Theoretical Models in Biology Gene Expression Studies Using
Mark Broom and Jan Rychtář Affymetrix Microarrays
Computational and Visualization Hinrich Göhlmann and Willem Talloen
Techniques for Structural Bioinformatics Handbook of Hidden Markov Models
Using Chimera in Bioinformatics
Forbes J. Burkowski Martin Gollery
Structural Bioinformatics: An Algorithmic Meta-analysis and Combining
Approach Information in Genetics and Genomics
Forbes J. Burkowski Rudy Guerra and Darlene R. Goldstein
Spatial Ecology Differential Equations and Mathematical
Stephen Cantrell, Chris Cosner, and Biology, Second Edition
Shigui Ruan D.S. Jones, M.J. Plank, and B.D. Sleeman
Cell Mechanics: From Single Scale- Knowledge Discovery in Proteomics
Based Models to Multiscale Modeling Igor Jurisica and Dennis Wigle
Arnaud Chauvière, Luigi Preziosi, Introduction to Proteins: Structure,
and Claude Verdier Function, and Motion
Bayesian Phylogenetics: Methods, Amit Kessel and Nir Ben-Tal
Algorithms, and Applications
Ming-Hui Chen, Lynn Kuo, and Paul O. Lewis
Published Titles (continued)
RNA-seq Data Analysis: A Practical Introduction to Bio-Ontologies
Approach Peter N. Robinson and Sebastian Bauer
Eija Korpelainen, Jarno Tuimala, Dynamics of Biological Systems
Panu Somervuo, Mikael Huss, and Garry Wong Michael Small
Introduction to Mathematical Oncology Genome Annotation
Yang Kuang, John D. Nagy, and Jung Soh, Paul M.K. Gordon, and
Steffen E. Eikenberry Christoph W. Sensen
Biological Computation Niche Modeling: Predictions from
Ehud Lamm and Ron Unger Statistical Distributions
Optimal Control Applied to Biological David Stockwell
Models Algorithms for Next-Generation
Suzanne Lenhart and John T. Workman Sequencing
Clustering in Bioinformatics and Drug Wing-Kin Sung
Discovery Algorithms in Bioinformatics: A Practical
John D. MacCuish and Norah E. MacCuish Introduction
Spatiotemporal Patterns in Ecology Wing-Kin Sung
and Epidemiology: Theory, Models, Introduction to Bioinformatics
and Simulation Anna Tramontano
Horst Malchow, Sergei V. Petrovskii, and
The Ten Most Wanted Solutions in
Ezio Venturino
Protein Bioinformatics
Stochastic Dynamics for Systems Anna Tramontano
Biology
Combinatorial Pattern Matching
Christian Mazza and Michel Benaïm
Algorithms in Computational Biology
Statistical Modeling and Machine Using Perl and R
Learning for Molecular Biology Gabriel Valiente
Alan M. Moses
Managing Your Biological Data with
Engineering Genetic Circuits Python
Chris J. Myers Allegra Via, Kristian Rother, and
Pattern Discovery in Bioinformatics: Anna Tramontano
Theory & Algorithms Cancer Systems Biology
Laxmi Parida Edwin Wang
Exactly Solvable Models of Biological Stochastic Modelling for Systems
Invasion Biology, Second Edition
Sergei V. Petrovskii and Bai-Lian Li Darren J. Wilkinson
Computational Hydrodynamics of Big Data Analysis for Bioinformatics and
Capsules and Biological Cells Biomedical Discoveries
C. Pozrikidis Shui Qing Ye
Modeling and Simulation of Capsules Bioinformatics: A Practical Approach
and Biological Cells Shui Qing Ye
C. Pozrikidis
Introduction to Computational
Cancer Modelling and Simulation Proteomics
Luigi Preziosi Golan Yona
PYTHON FOR
BIOINFORMATICS
SECOND EDITION

SEBASTIAN BASSI
MATLAB• is a trademark of The MathWorks, Inc. and is used with permission. The MathWorks does not warrant the
accuracy of the text or exercises in this book. This book’s use or discussion of MATLAB • software or related products
does not constitute endorsement or sponsorship by The MathWorks of a particular pedagogical approach or particular
use of the MATLAB• software.

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Library of Congress Cataloging-in-Publication Data

Names: Bassi, Sebastian, author.


Title: Python for bioinformatics / Sebastian Bassi.
Description: Second edition. | Boca Raton : CRC Press, 2017. | Series:
Chapman & Hall/CRC mathematical and computational biology | Includes
bibliographical references and index.
Identifiers: LCCN 2017014460| ISBN 9781138035263 (pbk. : alk. paper) |
ISBN 9781138094376 (hardback : alk. paper) | ISBN 9781315268743 (ebook) |
ISBN 9781351976961 (ebook) | ISBN 9781351976954 (ebook) |
ISBN 9781351976947 (ebook)
Subjects: LCSH: Bioinformatics. | Python (Computer program language)
Classification: LCC QH324.2 .B387 2017 | DDC 570.285--dc23
LC record available at https://lccn.loc.gov/2017014460

Visit the Taylor & Francis Web site at


http://www.taylorandfrancis.com
and the CRC Press Web site at
http://www.crcpress.com
Contents

List of Figures xvii

List of Tables xxi

Preface to the First Edition xxiii

Preface to the Second Edition xxv

Acknowledgments xxix

Section I Programming

Chapter 1  Introduction 3
1.1 WHO SHOULD READ THIS BOOK 3
1.1.1 What the Reader Should Already Know 4
1.2 USING THIS BOOK 4
1.2.1 Typographical Conventions 4
1.2.2 Python Versions 5
1.2.3 Code Style 5
1.2.4 Get the Most from This Book without Reading It All 6
1.2.5 Online Resources Related to This Book 7
1.3 WHY LEARN TO PROGRAM? 7
1.4 BASIC PROGRAMMING CONCEPTS 8
1.4.1 What Is a Program? 8
1.5 WHY PYTHON? 10
1.5.1 Main Features of Python 10
1.5.2 Comparing Python with Other Languages 11
1.5.3 How Is It Used? 14
1.5.4 Who Uses Python? 15
1.5.5 Flavors of Python 15
1.5.6 Special Python Distributions 16
1.6 ADDITIONAL RESOURCES 17

vii
viii  Contents

Chapter 2  First Steps with Python 19


2.1 INSTALLING PYTHON 20
2.1.1 Learn Python by Using It 20
2.1.2 Install Python Locally 20
2.1.3 Using Python Online 21
2.1.4 Testing Python 22
2.1.5 First Use 22
2.2 INTERACTIVE MODE 23
2.2.1 Baby Steps 23
2.2.2 Basic Input and Output 23
2.2.3 More on the Interactive Mode 24
2.2.4 Mathematical Operations 26
2.2.5 Exit from the Python Shell 27
2.3 BATCH MODE 27
2.3.1 Comments 29
2.3.2 Indentation 30
2.4 CHOOSING AN EDITOR 32
2.4.1 Sublime Text 32
2.4.2 Atom 33
2.4.3 PyCharm 34
2.4.4 Spyder IDE 35
2.4.5 Final Words about Editors 36
2.5 OTHER TOOLS 36
2.6 ADDITIONAL RESOURCES 37
2.7 SELF-EVALUATION 37

Chapter 3  Basic Programming: Data Types 39


3.1 STRINGS 40
3.1.1 Strings Are Sequences of Unicode Characters 41
3.1.2 String Manipulation 42
3.1.3 Methods Associated with Strings 42
3.2 LISTS 44
3.2.1 Accessing List Elements 45
3.2.2 List with Multiple Repeated Items 45
3.2.3 List Comprehension 46
3.2.4 Modifying Lists 47
Contents  ix

3.2.5 Copying a List 49


3.3 TUPLES 49
3.3.1 Tuples Are Immutable Lists 49
3.4 COMMON PROPERTIES OF THE SEQUENCES 51
3.5 DICTIONARIES 54
3.5.1 Mapping: Calling Each Value by a Name 54
3.5.2 Operating with Dictionaries 56
3.6 SETS 59
3.6.1 Unordered Collection of Objects 59
3.6.2 Set Operations 60
3.6.3 Shared Operations with Other Data Types 62
3.6.4 Immutable Set: Frozenset 63
3.7 NAMING OBJECTS 63
3.8 ASSIGNING A VALUE TO A VARIABLE VERSUS BINDING A NAME
TO AN OBJECT 64
3.9 ADDITIONAL RESOURCES 67
3.10 SELF-EVALUATION 68

Chapter 4  Programming: Flow Control 69


4.1 IF-ELSE 69
4.1.1 Pass Statement 74
4.2 FOR LOOP 75
4.3 WHILE LOOP 77
4.4 BREAK: BREAKING THE LOOP 78
4.5 WRAPPING IT UP 80
4.5.1 Estimate the Net Charge of a Protein 80
4.5.2 Search for a Low-Degeneration Zone 81
4.6 ADDITIONAL RESOURCES 83
4.7 SELF-EVALUATION 83

Chapter 5  Handling Files 85


5.1 READING FILES 86
5.1.1 Example of File Handling 87
5.2 WRITING FILES 89
5.2.1 File Reading and Writing Examples 90
5.3 CSV FILES 90
x  Contents

5.4 PICKLE: STORING AND RETRIEVING THE CONTENTS OF VARI-


ABLES 94
5.5 JSON FILES 96
5.6 FILE HANDLING: OS, OS.PATH, SHUTIL, AND PATH.PY MODULE 98
5.6.1 path.py Module 100
5.6.2 Consolidate Multiple DNA Sequences into One FASTA File 102
5.7 ADDITIONAL RESOURCES 102
5.8 SELF-EVALUATION 103

Chapter 6  Code Modularizing 105


6.1 INTRODUCTION TO CODE MODULARIZING 105
6.2 FUNCTIONS 106
6.2.1 Standard Way to Make Python Code Modular 106
6.2.2 Function Parameter Options 110
6.2.3 Generators 113
6.3 MODULES AND PACKAGES 114
6.3.1 Using Modules 115
6.3.2 Packages 116
6.3.3 Installing Third-Party Modules 117
6.3.4 Virtualenv: Isolated Python Environments 119
6.3.5 Conda: Anaconda Virtual Environment 121
6.3.6 Creating Modules 124
6.3.7 Testing Modules 125
6.4 ADDITIONAL RESOURCES 127
6.5 SELF-EVALUATION 128

Chapter 7  Error Handling 129


7.1 INTRODUCTION TO ERROR HANDLING 129
7.1.1 Try and Except 131
7.1.2 Exception Types 134
7.1.3 Triggering Exceptions 135
7.2 CREATING CUSTOMIZED EXCEPTIONS 136
7.3 ADDITIONAL RESOURCES 137
7.4 SELF-EVALUATION 138

Chapter 8  Introduction to Object Orienting Programming (OOP) 139


8.1 OBJECT PARADIGM AND PYTHON 139
Contents  xi

8.2 EXPLORING THE JARGON 140


8.3 CREATING CLASSES 142
8.4 INHERITANCE 145
8.5 SPECIAL METHODS 149
8.5.1 Create a New Data Type Using a Built-in Data Type 154
8.6 MAKING OUR CODE PRIVATE 154
8.7 ADDITIONAL RESOURCES 155
8.8 SELF-EVALUATION 156

Chapter 9  Introduction to Biopython 157


9.1 WHAT IS BIOPYTHON? 158
9.1.1 Project Organization 158
9.2 INSTALLING BIOPYTHON 159
9.3 BIOPYTHON COMPONENTS 162
9.3.1 Alphabet 162
9.3.2 Seq 163
9.3.3 MutableSeq 165
9.3.4 SeqRecord 166
9.3.5 Align 167
9.3.6 AlignIO 169
9.3.7 ClustalW 171
9.3.8 SeqIO 173
9.3.9 AlignIO 176
9.3.10 BLAST 177
9.3.11 Biological Related Data 187
9.3.12 Entrez 190
9.3.13 PDB 194
9.3.14 PROSITE 196
9.3.15 Restriction 197
9.3.16 SeqUtils 200
9.3.17 Sequencing 202
9.3.18 SwissProt 205
9.4 CONCLUSION 207
9.5 ADDITIONAL RESOURCES 207
9.6 SELF-EVALUATION 209
xii  Contents

Section II Advanced Topics

Chapter 10  Web Applications 213


10.1 INTRODUCTION TO PYTHON ON THE WEB 213
10.2 CGI IN PYTHON 214
10.2.1 Configuring a Web Server for CGI 215
10.2.2 Testing the Server with Our Script 215
10.2.3 Web Program to Calculate the Net Charge of a Protein
(CGI version) 219
10.3 WSGI 221
10.3.1 Bottle: A Python Web Framework for WSGI 222
10.3.2 Installing Bottle 223
10.3.3 Minimal Bottle Application 223
10.3.4 Bottle Components 224
10.3.5 Web Program to Calculate the Net Charge of a Protein
(Bottle Version) 229
10.3.6 Installing a WSGI Program in Apache 232
10.4 ALTERNATIVE OPTIONS FOR MAKING PYTHON-BASED DYNAMIC
WEB SITES 232
10.5 SOME WORDS ABOUT SCRIPT SECURITY 232
10.6 WHERE TO HOST PYTHON PROGRAMS 234
10.7 ADDITIONAL RESOURCES 235
10.8 SELF-EVALUATION 236

Chapter 11  XML 237


11.1 INTRODUCTION TO XML 237
11.2 STRUCTURE OF AN XML DOCUMENT 241
11.3 METHODS TO ACCESS DATA INSIDE AN XML DOCUMENT 246
11.3.1 SAX: cElementTree Iterparse 246
11.4 SUMMARY 251
11.5 ADDITIONAL RESOURCES 252
11.6 SELF-EVALUATION 252

Chapter 12  Python and Databases 255


12.1 INTRODUCTION TO DATABASES 256
12.1.1 Database Management: RDBMS 257
12.1.2 Components of a Relational Database 258
Contents  xiii

12.1.3 Database Data Types 260


12.2 CONNECTING TO A DATABASE 261
12.3 CREATING A MYSQL DATABASE 262
12.3.1 Creating Tables 263
12.3.2 Loading a Table 264
12.4 PLANNING AHEAD 266
12.4.1 PythonU: Sample Database 266
12.5 SELECT: QUERYING A DATABASE 269
12.5.1 Building a Query 271
12.5.2 Updating a Database 273
12.5.3 Deleting a Record from a Database 273
12.6 ACCESSING A DATABASE FROM PYTHON 274
12.6.1 PyMySQL Module 274
12.6.2 Establishing the Connection 274
12.6.3 Executing the Query from Python 275
12.7 SQLITE 276
12.8 NOSQL DATABASES: MONGODB 278
12.8.1 Using MongoDB with PyMongo 278
12.9 ADDITIONAL RESOURCES 282
12.10 SELF-EVALUATION 284

Chapter 13  Regular Expressions 285


13.1 INTRODUCTION TO REGULAR EXPRESSIONS (REGEX) 285
13.1.1 REGEX Syntax 286
13.2 THE RE MODULE 287
13.2.1 Compiling a Pattern 290
13.2.2 REGEX Examples 292
13.2.3 Pattern Replace 294
13.3 REGEX IN BIOINFORMATICS 294
13.3.1 Cleaning Up a Sequence 296
13.4 ADDITIONAL RESOURCES 297
13.5 SELF-EVALUATION 298

Chapter 14  Graphics in Python 299


14.1 INTRODUCTION TO BOKEH 299
14.2 INSTALLING BOKEH 299
14.3 USING BOKEH 301
xiv  Contents

14.3.1 A Simple X-Y Plot 303


14.3.2 Two Data Series Plot 304
14.3.3 A Scatter Plot 306
14.3.4 A Heatmap 308
14.3.5 A Chord Diagram 309

Section III Python Recipes with Commented Source Code

Chapter 15  Sequence Manipulation in Batch 315


15.1 PROBLEM DESCRIPTION 315
15.2 PROBLEM ONE: CREATE A FASTA FILE WITH RANDOM SE-
QUENCES 315
15.2.1 Commented Source Code 315
15.3 PROBLEM TWO: FILTER NOT EMPTY SEQUENCES FROM A
FASTA FILE 316
15.3.1 Commented Source Code 317
15.4 PROBLEM THREE: MODIFY EVERY RECORD OF A FASTA FILE 319
15.4.1 Commented Source Code 320

Chapter 16  Web Application for Filtering Vector Contamination 321


16.1 PROBLEM DESCRIPTION 321
16.1.1 Commented Source Code 322
16.2 ADDITIONAL RESOURCES 326

Chapter 17  Searching for PCR Primers Using Primer3 329


17.1 PROBLEM DESCRIPTION 329
17.2 PRIMER DESIGN FLANKING A VARIABLE LENGTH REGION 330
17.2.1 Commented Source Code 331
17.3 PRIMER DESIGN FLANKING A VARIABLE LENGTH REGION,
WITH BIOPYTHON 332
17.4 ADDITIONAL RESOURCES 333

Chapter 18  Calculating Melting Temperature from a Set of Primers 335


18.1 PROBLEM DESCRIPTION 335
18.1.1 Commented Source Code 336
18.2 ADDITIONAL RESOURCES 336

Chapter 19  Filtering Out Specific Fields from a GenBank File 339


19.1 EXTRACTING SELECTED PROTEIN SEQUENCES 339
Contents  xv

19.1.1 Commented Source Code 339


19.2 EXTRACTING THE UPSTREAM REGION OF SELECTED PRO-
TEINS 340
19.2.1 Commented Source Code 340
19.3 ADDITIONAL RESOURCES 341

Chapter 20  Inferring Splicing Sites 343


20.1 PROBLEM DESCRIPTION 343
20.1.1 Infer Splicing Sites with Commented Source Code 345
20.1.2 Sample Run of Estimate Intron Program 347

Chapter 21  Web Server for Multiple Alignment 349


21.1 PROBLEM DESCRIPTION 349
21.1.1 Web Interface: Front-End. HTML Code 349
21.1.2 Web Interface: Server-Side Script. Commented Source Code 351
21.2 ADDITIONAL RESOURCES 353

Chapter 22  Drawing Marker Positions Using Data Stored in a Database 355


22.1 PROBLEM DESCRIPTION 355
22.1.1 Preliminary Work on the Data 355
22.1.2 MongoDB Version with Commented Source Code 358

Section IV Appendices

Appendix A  Collaborative Development: Version Control with GitHub 365


A.1 INTRODUCTION TO VERSION CONTROL 366
A.2 VERSION YOUR CODE 367
A.3 SHARE YOUR CODE 375
A.4 CONTRIBUTE TO OTHER PROJECTS 381
A.5 CONCLUSION 382
A.6 METHODS 384
A.7 ADDITIONAL RESOURCES 384

Appendix B  Install a Bottle App in PythonAnywhere 385


B.1 PYTHONANYWHERE 385
B.1.1 What Is PythonAnywhere 385
B.1.2 Installing a Web App in PythonAnywhere 385
xvi  Contents

Appendix C  Scientific Python Cheat Sheet 393


C.1 PURE PYTHON 394
C.2 VIRTUALENV 400
C.3 CONDA 402
C.4 IPYTHON 403
C.5 NUMPY 405
C.6 MATPLOTLIB 410
C.7 SCIPY 412
C.8 PANDAS 413

Index 417
List of Figures

2.1 Anaconda install in macOS. 21


2.2 Anaconda Python interactive terminal. 23
2.3 PyCharm Edu welcome screen. 35

3.1 Intersection. 60
3.2 Union. 61
3.3 Difference. 61
3.4 Symmetric difference. 62
3.5 Case 1. 65
3.6 Case 2. 66

5.1 Excel formatted spreadsheet called sampledata.xlsx. 93

8.1 IUPAC nucleic acid notation table. 147

9.1 Anatomy of a BLAST result. 181

10.1 Our first CGI. 216


10.2 CGI accessed from local disk instead from a web server. 217
10.3 greeting.html: A very simple form. 217
10.4 Output of CGI program that processes greeting.html. 218
10.5 Form protcharge.html ready to be submitted. 220
10.6 Net charge CGI result. 222
10.7 Hello World program made in Bottle, as seen in a browser. 224
10.8 Form for the web app to calculate the net charge of a protein. 229

11.1 Screenshot of XML viewer. 244


11.2 Codebeautify, a web based XML viewer. 245

12.1 Screenshot of PhpMyAdmin. 258


12.2 Creating a new database using phpMyAdmin. 262
12.3 Creating a new table using phpMyAdmin. 264

xvii
xviii  LIST OF FIGURES

12.4 View of the Student table. 266


12.5 An intentionally faulty “Grades” table. 267
12.6 A better “Grades” table. 267
12.7 Courses table: A lookup table. 268
12.8 Modified “Grades” table. 268
12.9 Screenshot of SQLite manager. 277
12.10 View from a MongoDB cloud provider. 281

14.1 A circle with Bokeh. 302


14.2 Four circles with Bokeh. 303
14.3 A simple plot with Bokeh. 305
14.4 A two data series plot with Bokeh. 306
14.5 Scatter plot graphics. 308
14.6 A heatmap out of a microarray experiment. 310
14.7 A chord diagram. 312

16.1 HTML form for sequence filtering. 327


16.2 HTML form for sequence filtering. 328

21.1 Muscle Web interface. 350

22.1 Product of Listing 22.2, using the demo dataset (NODBDEMO). 356

A.1 The git add/commit process. 369


A.2 Working with a local repository. 370
A.3 Working with both a local and remote repository as a single user. 379
A.4 Contributing to open source projects. 383

B.1 “Consoles” tab. 386


B.2 The “Web” tab. 386
B.3 Upgrading domain type option. 387
B.4 Select a web framework screen, select Bottle. 388
B.5 Select a Python and Bottle version. 389
B.6 Form to enter the path of the web app. 390
B.7 The sample web app is ready to use. 390
B.8 The “File” tab. 391
B.9 Form to create a new directory in PythonAnywhere. 391
B.10 View and upload files into your account. 391
LIST OF FIGURES  xix

B.11 Front-end of the program to calculate charge of a protein using


Bottle and hosted in PythonAnywhere. 392
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WRIGHT COL'XTY, IOWA. 417 Jelske C'ranier and llattie
l".gger.s were married on X(i\-enilier 13, 1873. Airs. Cramer is a
daughter of Herman and Taulga ( Steinljlock ) l-lggers. To Mr. and
Mrs. Cramer have heen horn eleven children, namely: Anna, Thresia,
Minnie, Margaret, Herman, hlrnest, I'.lsie, John. Jelske, Dalla and
Kay. Anna, the eldest ihuighter, has remained single; Thresia niarrietl
J. G. Groenenwold, and is the mother of t\\(_i children, Gertrude and
Xettie; Minnie married 1-Ted I'ahlman, and to them four children
were horn, these i)eing Jelske. Clara, Xettie and lidna ; Margaret
married J. riroenenwold, and their children are Etta and George;
Herman hecame the hush;ind of Sophia Schmidt; Earnest married
Cleo Chapman; Elsie married William Meyer; the other children are
single. Mr. Cramer, since his residence here, has hecome identihed
with various puhlic interests, one of which is the schocjl system, of
which he has heen a director. His ]5olitical affiliations ha\e heen with
the Democratic party, of which he has ijeen a prominent memher.
Such has l>een Mr. Cramer's fitness for public ser\ice that he has
heen one of Clarion's most ixjpular schocjj directors. He has given
much time and study to the (juestion of education, and is keenly
interested in all that pertains to the welfare of the town in which he
lives. Both he and Mrs. Cramer are active members of the German
Lutheran church. HOX. A. S. CHAPMAN. One of Wright county's best-
known citizens was A. S. Chapman, who came to this county in
1869. He was horn in Penobscot county, Maine, .May 27, 1846, son
of Winthrop Chapman, a native of the same county and a son of
\\'inthrop Chapman, Sr., who was a pioneer in Exeter, Maine. He was
a man ol much wealth, fie was of Scotch ancestry. The mother of A.
S. Chapman was Caroline (luistman) Chapman. A. S. Chapman's
father died on April 4, 1S81. .\. S. Cha])man was reared in his native
county, educated at l'",xeter Academy and later engaged in teaching
in several towns. In 1869 he came to Wright county and located in
the southern part of this county, and kept "bachelor's hall." There he
lived anrl became one of the county's wealthiest men and spent the
rest of his life, dying in October. i88r). He owned over one thousand
acres of \'alualile Wright county land, and was an extensive stock
raiser and feeder. He was a stanch Republican and represented this
(27)
4Io WRIGHT COUXrv, IOWA. cuunty in the luwa
Legislature, Ijeiiig elected in 1887 and ^er\etl in the 'rwenty-seeuud
General .\ssenil)ly. lie was a nio^l excellent lawmaker. .Mr. Chapman
wa> twice niarrietl, lirst tu lunnia W. Llark. 1)_\- whom he had three
children. His wife died in l.Jctol)er, itate. In the >pnng of 1874 he
removed to Wright county, L)wa, and purchased one hundred and
.Mxtv acres in Troy township. Tliis propert}- was increased to three
hundred and twenty acres, which he cultivated until l(,uo, his
retirement taking place at that time, .\fter fori) -three )ears i.if
general farming, he retired to the town of I'.agle (iro\e, Iowa, where
he held several towiishiii olticev Of the ten cinklren born to Mr. and
Mrs. l-'.ugene -\. .\lleu, eight are ikjw hving in Wright county, Iowa.
Mehin (Claiip) .Mien was a native of Wisconsin and was married in
that state. lulgar A. Allen received his education in the common
schols of Wright county, Iowa, and after rmishing the necessary
branches lie taught for several years, or until he was twent)-two
years of age. At that time he purchasefl one hundred and si>;t)-
acres of land, with the intenti
WJUGllT COUNTY, IOWA. 4I9 agricultural pursuits until ujii,
when he cugaycil in the autuniohile husiiK'ss, following tliis until
1914. Un Xoxcnihcr 3. 1914, he wa^. elected to the oHice of county
treasurer and his duties in that cajtacit)- heyan on January _', 1915.
While engaged in farnnng Mr. .Mien served his townshii) hy acting as
townshii) clerk autl trustee of Trov township, and the disijatch with
which he discharged all duties demonstrated his ahilit)' as a leader in
the more nnjjortant offices of trust to which he was later elected. In
the niunlh of Xoveinher. iSqj, i^dgar .\. .\llen was united in marriage
to Alary li. Lewis, tlaughter of Richard and jane (I'ugh) Lewis, and to
them have heen horn three children: hdva Al., \'ernice [. and Juigene
R., all of whom arc at home. Edgar ,\. .\llen is a meniher of tlie
Alethodist Episcopal church, in which he acted as trustee f'et unhoru
to accord a full measure of appreciation for the immortal characters
carved out hy the .\mcrican solilier, among whom was the venerable
Uavid L. Cupjiett, formerly a farmer, merch;int, hanker and public-
spirited man of affairs. lioru on December 25, 1S41, in Bedford
county, 1 'eniisylvania, David L. Qippett, is the son of David A. and
I'.lizabeth (Alickles) Cuppett, who were natives of 1 'eniisylvania and
who married in Bedford count v. David A. Cni)i)ett was the son of
Isaac (."ujjpett, who, it is believed, emigrated from llollan.l to
.\merica. David .\. (,u])])ett had enlisted for service in the
to scr ■ice. He was a hildre 1, six of whon _> the faniil)
settled ii >r foil owed his trade and serve I there as 420 WRIGHT
COUNTY, IOWA. Ulack Hawk War, but his company was not calletl
blacksmith by trade, and was the father of twelve lived to maturity
and all of whom went west. In li Iowa, locating in Delaware county,
where the fat He took an active part in the politics of Colesbu justice
of the peace for eleven years. David L. Lu]jpett received a good
common-school educaticiU, and when old enough, obtained work in
a pottery, where he was employed for four years, until September
10, 1861. when he enlisted at Dubuipie, Iowa, in Company G, Ninth
Regiment, Iowa Volunteer Infantry. His first service was under
General Curtis at the battle of Pea Ridge, Missouri, on March 6, 7
and 8, 1862. This regiment lx)re the brimt of that battle, and his
brigade lost more men than all of the other regiments c(jmbined. On
March 7. i86j, Mr. Cuppett received a wound in the right shoulder
and was sent home on a furlough for tw(j months. He then started
back to join his old comiKiny, Init IkuI proceeded onl}- as far as St.
Louis, when he was again sent home. He remained at home until
July 8, 1862, when he joined his company at Helena, Phillips county,
Arkansas. In July, 1862, the western campaign had become
extremely bitter, and following Mr. Cuppett's return the regiment
took part in the engagements of Chickasaw Bayou, which was the
only defeat the regiment ever suffered: Arkansas Post; the siege of
V'icksburg; Jackson, Mississip])i ; Brandon, Mississippi; Cherokee,
Mississippi; Lookout Alountain. 'rennes>ee: Missionary Ridge,
Tennessee; and Ringgold, Georgia. Mr. Cui>pett was sent home on a
thirty-day furlough in 1863. and was honorably discharged on
January i, 1X64, at Wmidville, Alabama. He again re-enli.sted on the
same day, in the same company and regiment. Afterward he took
jiart in the battles of Reseca, Georgia; Dallas, Big Shanty and
Keiiesaw Mountain. .\t Kenesaw Mountain he was wounded by a
piece of a shell, which struck him in the shoulder. He served with
General Sherman in his campaign fnjm .\tlant;i to tlie sea, and was
in the following battles; Nickajack Creek, .\tlanta, Rzra Church,
Jonesb(jro, r.ovejoy Station, Little River, siege of Savannah, Wateree
River; Columbia, South Carolina; Bentonville and Raleigh, Xorth
Carolina. Mr. Cuppett took part in the Grand Review, at Washington,
D. C, and was honorablv discharged at Louisville, Kentucky. July 18,
1865. In May, 1864, Mr. Cuppett was promoted to the rank of
corporal, but hefd this rank inily two days, when he was ])romoted
to orderly sergeant.
WKIGUT CUl'NTY, IOWA. 42I lie was later promoted to
second lieutenant and ^erved for a short time in this capacity, but
never recei\eil his commission. After Mr. Cuppett's discharge he
returned to his home Ijut tlid not remain long until he removed to
Dul)U(|ue, Iowa, where he was taken in as a partner by his former
employer in the pottery business. Mr. Cuppett continued in this
business for two and one-half years and then returned to Colesburg,
where, in partnership with Trueman ]'. Wells, purchased H. P.
Wright's general store. They operated this store in partnership for
two and one-half years and .Mr. Cuppett then came to Wright
county, in the fall of 1871, and located in Belmond, where he
engaged in the hardware business in i)artnership with \'\. S.
llulibard. This jiartnership continued for se\'eral }ears, when linally
Mr. Cuppett jjurchased Mr. Hubbard's interest and operated the store
alone, in the meantime ha\-ing added a stock of implements. In iSgi
Mr. Cuppett sold the hardware store to \'al Greessey, and devoted
his attentioiCto the implement business until 1906, when he sold the
implement business to Harry Tyrrell. Mr. Cu])pett also owns several
farms, among them one liundred and sixty acres in South Dakota,
one iiundred and sixty acres in Belmond township, Wright cuunty,
and lias owned other has also owned sexeral tow: ^tate except his
home and one 1 the north part of lielmond irst National anil tlie
liclniom iSr,6. David L. Cuppett was n )liard, who wa^. l).irn on Ma\
irents were liezekiah and Sarah (Burgess) Hi icut, who removed to I
'ennsylvania and later .\lr. and Mr>. I'upiiett were married by the R
marriage there ha\e been born six children, fi of whom are living.
.\rthur B., b Jennie Rolbeck, and they ha\e three Ha/.el is married,
l.orenza 1-".., bor llrewsaugh, and they ha\c two cliik later married
K. K. Bailey, and the; born on March -'5, 1S7.:;, married b'-.l Cli iva,
b'rank, Mae and .\rthur. S .\lbert luiglet, and they h;i\e three childr
l.ee 11., born on .\ovember 4, 1S7.), ,li S., born on .\ugust 18, 1884,
died on Xovember 7, 1884. farms at otller times. H( sold most ; 0 f hi
is real est; and fixe ; acr es i :)f land in stockholder 1 in b -oth the
1m ( )n .^ ^ep teni iber ..'(,. i.^ Iowa, to l.u cret :i;i K. Hul burg,
low a. am 1 whose p; bard, nat i\'e S 0 f Connect' Iowa in t he ear
1_\' forties. (reorge I. arl. :in. To their pr operties. Init has itlK ;r
house and I lot Mr. Cupp ett is a Sta .te Bank. :u-ri ed in Ci desk 'iirg,
-'.V 1848, r n C. 1.1 es1 (ju Septen iber 19, 1868, married ildren,
llazel , Blanche and David T. ,n Marcli 1 , T871, married Ceorge n,
\'era and Geraldine. l.orena F.. lave one chi Id, B.eatrice. Mary A.,
hristie. and the\' ha\e four children. I'.., born on May 2:;, 1877,
ni.arried Iren, l''.dwin. Knth 1,. .and .an infant. ed on Se|ite: inl)er
10, 1
422 WRIGHT COUNTY. U)\V.\. Mr. L'lippett is a nicniiicr of
tlie Masonic Iraternity and tiic Grand Army of the Jvlcpuhlic. lie lias
lield all of the iniporlant oflices in the Cirand Arni)- of tiie kepnl)lie
and for the last ei-lit years has served as eomniander of tlie post, lie
was also a ciiarter ineniher of iielniond i.odye, Independent Order of
Odd l-'elJows, iiavin- lieen nntiated nito the order winle m the army.
Later he helped or-anize the iielniond lod-e, lint has since dropped
ont. lie was a charter inenibcr of Whited I'ost Xo. 24J, of P.elmond.
C.rand Army of the Kepiililic. Mr. (,'np])ett is a Re]nil)lican in jiolitics
and lias ser\ed in many positions of Irnst and re.sponsijjijity. He has
lieen township trustee, school treasurer and assessor of I'leasant
township. Since remo\int^- to liehiioiid, he has filled an nne.xjjired
term as ina)'or. has ser\ed in the conncil, as city treasurer, as school
treasurer, and in other ca])acities. Mrs. ("uppetl is a niemher of the
Oon^t;-rei;ational church. Micii.M';]. .\X(1i-:lo mkkmlsox. Michael
An-el.j Miekelson is a man so widely known and .so l)eloved tiiat a
record of his life will lind welcome in many hearts, this in itself
coustituliii!.^ an einiahle trihute. While much ot his lime has been
given to agricultural jmrsuits, in which he has taken a deej) interest,
his mental horizon Is hroad enough to include subjects of the imblic
good and public service, and in these perhaps Mr. Alickelson found
his greatest source of pleasure. .Michael .\ugelo Miekelson was born
..n December _^o, 18.15, i" N'orwaw and is the son of Ola and
.\ngeliiie Mickels,,n, both natixes of that countrw Ola Miekelson was
a farmer in Xorway, and came to this country in uSsCi, locatmg in
(ireeii count), Wisconsin, where he had engaged in farming only a
\ear when both he and his wife died from the effects of cholera,
passing awav withm twehe hours of each other. One of their
children, an infant, died at the same lime. Lura, Michael and Xewton
are the reniaimng members of the family, the last named son imw
resine year's residence with this family, according to the custom of
that day, he was bdiind out to a man b\- the name of Stewart. The
boy engaged tn w
wintair coi'nty, iowa. 423 Michael A. .Mickclson enlisted fur
regular ser\ice in the Civil War un l'"ehriiary jj. 18O5, at Alhany,
Wisec ln^in, serving until Xuvenil)er, 18O5, in Cdinpau)' Ci, h'orty-
ninth Regiment, Wisconsin XOlunteer Inlantr}-. lie jonied the
regiment at Alaclisun, Wisconsin, then did guard dut}' at Rolla,
.Missom-i, and in the latter part of Se[)teml>er, iS()5, was sent with
his comrades to do guard duty in St. Louis. At the age of twent_\-
one ^Michael A. Alickelson rented a farm of forty acres which he
culti\ated for the period of one year. lie then increased his rented
property to t\\ arrangement coutuiued luitd he hail taught eight
term^, lie then toi^ik uij his rcMdence on one hundred and si.\t\-
acres of land in Woolstock townshii), this county, for which property
he paid twenty-hx-e hundred dollars, which he had saxeil h\- the
comhined occupation (if farmmg and teaching in Wisconsin. On
Ocloher 31, 1S77, Michael A. .Mickelson was married to I'annie Fern
Fleek. a daughter of h'.chnund Thiimas and Sarah (Howen) hdeek.
Mr. Mickelson's wife was Ixnn in Wisc(jnsin, her father ])eing a nati\e
of \irginia, and her mother was horn m renusvlvama. These worthy
people were married m Wisconsin, to which state Mr hdeek came
when a yotmg man and began farming in (ireen county, where he
li\'ed the remainder of Ills life. 'Iliis cou]ile were the parents of
eleven children of whom Mrs. Mickelson was the third horn. She has
hve brothers and sisters living. The morning following the wedding
of Mr. and Mrs. Mickelson these iKirses and a well filled wagon,
arriving m Woolsack township on Xovemher 9, 1S77. The\ were
guests of Mr. Mickelson's brother, Xewton, until arrangements could
be made for them to mo\e on their own laiul. One of the lirst things
which Mr. Mickelson did was lo plant a number of beautiful trees
which lia\e made their home farm .juc (d' the most attracti\e in this
section of the state. f'y hard work and persexerance ^fr. and ^vFrs.
Mickelson ha\e ac(|uired four hundred and eight\- acres (d" splendid
farm land, ami one
424 WRIGHT COUNTY, IOWA. Tlie confulence in wliicli Air.
Alickelson is held in this cunimunity is evidenced by the fact that he
has held a nuniljer of public oftices. He was for some time township
trustee, again was appointed road supervisor, and later president of
the school board of Woolstock township. He was also treasurer uf
the district school of Eagle Grove for two years; he served ten years
as cuuncilnian and for four years uf this time was may(jr of Clarion.
Mr. and Airs. Alickelson have a beautiful home, modern in every
respect, located near the court house in Clarion. This is the scene of
many pleasant social gatherings, fur the owners are among the
fortunate type oi people who have friends because they are friendly.
Airs. Alickelson is a woman of culture and relinemeiit. Air. Mickelson,
who is a Rei)ublican, is an. enthusiastic member of the Grand Army
of the Republic. He is a member of the AIas(;nic lodge, the. chapter,
council and commandery, and also is a member of the Alystic Shrine.
In even this incomplete study of the life of Alichael A. Alickelson, one
discovers the elements which go to make up what in more
conspicuous lives is called greatness. Here is a man who was willing
to die for his country if need be; in peace, he has lived for his
country, and by his [jersonality and his genial nature has been a true
friend and real inspiration to all with whom he has come in contact.
JOHN CAAirBI'LL .\ native uf Canada, jolni Campbell, like his w(jrtliy
parents, has been content to follow a well-directed course
throughout life, liurn and reared on the farm, he has devoted bis
entire time and attention to agricultural pursuits, and has made a
record which it will ])e an honor to band ilown to his children,
.\lthough encountering obstacles and disappointments, he has
refused to become disheartened, anil has pressed forwanl until he
has become one of the leading farmers in this county and has had
the honor of ha\ing held all of the township ofticcv J(,hn Campbell
was born on Alarch j^, 1X45, in Ontario, Canada. David Campbell,
father of John Campbell, was born in the state of New ^'ork. When
he was a small child bis ])arents moveil to Ottawa, Canada, and
there he received his education and helped bis father on the farm
until bis si.xteenth )ear. He was then employed a^ a farm laborer for
a number of vears and bv the time be was twentx-five vears of age
was alile
WKUaiT COL'NTY, IOWA. 4-'d to jnirchast farm land in
Ontario witli muney he liad earned and saved, ■|"liere lie farmed
nniil 1S50, when he removed to the United States. lie rented a farm
in l,a[)eer county, .Miclni;an. where he h\ed until iS()5. He then
eame to Wright eounly. this state, loeatini; in I'leasant townshiji,
where he farmed for a year or two and later hought a farm of eighty
acres in Iowa lowiiship. .\fter li\e years of residence there he and his
family moved to a farm which he rented in !>elmond township,
where he li\'ed until his death, which occurred in 1SX7. His wife, who
hefore her marriage was Margaret McMartm, \va^ horn in Osgood,
Canada. .She died in 1850, leaving four chddren, who are now
living. .\ Fifth child is deceased. Her hrother, Thomas, served in the
C\\\\ War and was killed. Her three remaining hr(jthers are still
li\'ing in Canada. John Camphell went to school in the state of
Michigan and afterward was em])loyed in farm work until he came
to this county, .\fter his marriage, Januar}- i-)th, he honght a farm
of eight\- acres, which he has suh>e(|uently increased to an estate
of three lumdred and sixty acres, where he has hecome a general
farmer and stock raiser. On j.uuiary 14, 1S71, John ranii)l)ell was
united in marriage to .\.ngeline .Morris, daughter of Dr. J. 0. ami
I'hoehe U. ( ilahcock ) M.irris. John L. Hahcock was horn in .Mmont,
.Michigan, although her ])arents were nati\'es of other states, the
father id' I'ennsyhania and the mother of .\'ew N'ork. where Doctor
Morris was educated. When about twenty-live _\■ear^ of age, Mr.
Morris started a store in .Mmont, Michigan, and after three years in
that business he took a ten-year contract for cutting and delivering
logs. He then took u]) the ])ractice of medicine, and in 1864 came
to W'right countv, where, after a year's residence near ISehnond, he
started a medical practice, which suhseipiently became e\teusi\'e. In
1880 he and his faniilv moved to Scrantou, Iowa, where thev lived
until the time of his death, in 1888. lli.s wife died in January, M;I5.
I'.leven . d' their thirteen children are still living. To Mr. and Mrs.
John ( amiihell have been Immii three children, namely; William T. is
the husband of .\liiia Sougstadt : John D. married Ciertrude Dice,
who is the mother of two children. Rhea and Tleiie; Cora l^veline,
the youngest child, died when li\e years old. Mr. and ^Irs. Campbell
are iirominent members of the Methodist l^piscop.-d church. Air.
(."amphell is a man who is well read and has been for maiiy years
active in ])ublic atlairs. He has held nearly all the offices which this
townsliip has to ofTer. Mr. and Airs. Camphell fill an important place
in the coniiiiunit\- in which thev have lived so many years and have
shown
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426 WRIGHT COUNTY, IOWA. practical interest in its


welfare by sup[)urting its worth)- enterprises. Air. genial nature, and
ln> Ingh nuiral standards have given hmi the respect of all who
know him. E. E. BliST, .M. U. Dr. E. E. JJest, of Clarion, Wright
county, Iowa, is the personification of courtesy and kindness and his
concentration has made him a master in the art of healing; his
practical L'hristianit_\- ha.-- hrought him in close touch with the
hearts of men and his toleration for their weaknesses has made of
him a true friend to tlnjse in neeil. h:. E. Best is one of si.\ children
horn to the union of W. C. and .Vnn Kliza (C'lingman) liest, he a
native of l'enn--yl\ ania and she of Ohio. The birth of ]•;. i;. I lest
occurred on March 4, 1858, m l'reep(jrt, Illinois. W. C. ik'St remametl
m his native state until se\eiUecn \car>
WRICriT COL'NTY, lUWA. 427 was engaged in Cliicagu,
Illinois, he completed the course in the College of riivsicians and
Surgeons, graduating from the same in i8i)i;. ISecoming interested
in iowa as a future lield for his meilical practice, he renioxed to
Clarion in njoi, and has since received a large i)atronage from the
citizens uf that town. In iiT, he immigrated to the Cmlcd .St.ates and
located near ila/.el Crceii, Wiscoiisiu, where he was cmplovc.l m the
ca])acity of farm hand for a period of three \ears. In .May, iS(>
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4^8 WRIGHT COUNTY, IOWA. indepeiuleiit efforts in


comiiiercial pursuits, he eugaged in tlie grain brokerage liusiness. liut
in icS()i, after meeting with unusual success for others, lie began
buying for himself, and in 1900 included stock buying in his other
interests. He buys, on an average, one luuidred carloads of stock
each j year. That he has won a place of no mean mention, is
evidenced b)' the i fact that he was elected and ser\ed as the mayor
of Clarion co\ering a | period of eight years, and also served as city
assessor for f(nir years. 1 In 1886 I'eter II. (loslin was united in
marriage to Clara Lynch, daughter of b'dmund and Jane Lynch, and
the\- arc the parents of two children, Leroy !'. and Ldmond Clare,
I'obtically, I'eter IL Goslin is an ardent Democrat, and his religious
inspiration is receivetl from the creeds of the Cath(jlic church, which
dem inunation receives hi's earnest and active support. He is a
member of the Knigiits of Cohunbus ancl is held in liigh regard by
the members of that order. ( Jn l-'ebruary -'5, 1015, he was
appointed postmaster (jf Clarion, Wright coimtv, Iowa. C. H.
AL\UTI\. One of the first men to locate in Ijoone township, tliis
count)', and who became a wealthy, enterprising farmer and lived a
good and U[)right life, was "Uncle Henry" .Martin, as he was usually
called. C. H. .Martin was born in Gloucester, luigland, in January,
j8i8, and died in B(jone township, this cmnity, in 1893. He made his
own way through life unaided by wealthy relatives or friends. He was
the son of a woolen manufacturer, who having lailh m .\uierica
brought his lamdy hither and located in Ohio, the wife and mother
dving ui Lnglaud. The lather had married the second wife before
emigrating from Ivngland. Young C. 11. .Martin worked at farm labor
in Ohio, saved his money and detcrmine
WRIGHT COUNTY, IOWA. 429 WILLIAM L ROSLCRAXS. An
active lite is conducive tu a long one and sincere interest in public
affairs engenders the confidence and trust of une's fellow citizens.
I'osit:uns uf trust may be gained, but never held lur any length of
time, by those unwortln uf them, su the life uf William 1. Rusecran>
affords much food fur retiection, lor his career is strewn with
evidence of public contidence and trust, anil the record of his many
achie\einent.-, contains many examples uf civic pride and
betterment. William 1. Kosecrans is une of seven children born tu
Judge JNIarmaduke 1'. and Luc_\- (Green) Rosecrans, and his birth
occurred on August i8, 1S62, on a farm in Hancock count\ , Iowa.
.Judge Marmaduke i'. Rosecrans, with his family, came to Iowa
during the forties and settled in Sigourney, kjwa, a town located in
the southern part of the state. The names of the ijrothers and sisters
of William 1. R(jsecrans follow : Charles, who served in the Union
army and met his death at Memphis, Tennessee, while fighting for
his country; Julia, wife of (iurley G. I'ritchard and iiuw living in Lus
Angeles, Califurnia; lulgar J., who married Jennie Speers, of Clear
Lake, Iowa, and is now living in Seattle, Washington; Alice C, wife of
Dr. (L F. McDowell, resides at Clear Lake, b.wa; Idora 1-:., wife uf Dr.
Z. C. Cireen, of (jarner, Iowa, where her death occurretl in icSHH;
Harry M., who married Ida \\'(jud, (jf Clear Lake, luwa, and n(jw
resides in Dubuipie, William 1. Rusecrans, remuved with his ]iareiits
to Cle.ar Lake, Iowa, in i8()(). and receued hi^ education in the
jfublic schools of that jjlace, linishing with a course in ISailey's
Ijusiuess College, at Dubuque, biwa. After this theoretical training,
he recei\ctl his jiractical training in the business house of hiv brother-
iudaw. (i. (',. Tritchard, his service beginning m 1S78 and rounding
tu completion 111 1(8X5, ;it which time he ])urchased the busines^
from lii> emi)loyer and fornud a partner>hip with C. C.. I'ritchard.
for the sale of general merchandise. In i8ij(S the partnershi]) was
dis>(jl\e(l and William I. Kosecrans entered the shoe business,
which was comlucted for seven years, in Relnioiid. biwa. During
these- years he was also interested in the lohnsun M- Kusccrans
Crain Com])an\-. of which he was ,1 member. This coni]iany
o]X'rated a chain of i-le\ators throughout the state of Towa. In 1005
the shoe Imsiness was disposed of and Mr. Rosecrans devoted his
entire time to the successful operation of the grain business, which
he has conducted to the |)resent lime.
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430 \VRU;UT CUL'NTY, IOWA. In iSSo \\ illiani 1, Uiisuciaii^,


wa-, muted in inarriai;c U> I'atlicriiK' G. I'liKii, (lau.^lUcT of William
aii.l (iittic ( Dummmul ) l-iiKh and of tins union two dnldrcn were
l)orn : Leo .M., who resides m ]j>i An-eles. was married 111 July,
iliier ni the Iowa \'alley State Hank, which hecanie the I'lr^t Xatmnal
l'.:mk of I'.ehiKiiul. h\ the L'mted States h'xpress ('(impany, at
iielmond. Iijwa. lie has also been interested in the great
development of the West and is the owner of \alual)le land holdings
in i.nva and Dakota, consisting of two iumdred and eight) acres in
the counties of Wright, near Cornelia, llancock, near (larner, m low.i,
and four farms consisting of six hundred and forty acres, in Richland
cciimty, Xorth Dak.na. William 1. Uosecrans has found ani])lc time ti)
imrsue the pleasant things of life and is a much traveled and widel\-
read man hut ahove ail. he is just and humane, sociahle and kind,
and is the kind of man one kwes to meet, lie is a memlier of King
Solomon Lodge Xo. jio. .\ncient h'ree and Acce])ted Masons, also a
Knights Temiilar and a nohlc of the Mystic Shrine. L'. B. SHELDON.
The career of \'. Ik Sheldon, a native son of this county, is one of
individual and unaided eHort, and indicates the success to wliich the
.American hoy can climl) when he possesses within himself the
necessary qualifications. .Mr. .Sheldon descends from a f.amily
whose members have inspired admiration and respect for several
generations, and his father set for his cliildren an example which
they have followed, an examjile of bravery and lovalty, for he was a
L'i\-il War veteran. I'. 1'.. Slieldon, who has occupied a conspicuous
]ilace in local hanking circles, was l)orn on December lO, i8(')6 in
N'ernon township, of this county, and is the son of Charles 1'. and
Isabel (Stevenson) Sheldon. They were natives of l-~.sse\ county,
.Xew ^'ork, where the\ were m.irried. The father, a farmer, came to
this state in 1N34, and when the life of the nation was
WmClIT COUNTY, U)WA. 431 llireateiiecl, lie enlisted in the
Secoiul Kan.-^a^ I'axalry, Irum C'laMnn cuunty, Iiiwa, remaining in
service from the tall ot iNdi nntil the cl(j>e ut the war. In order for
hini to enli>t I'roni Kansas, it waN nece^s.ir) lor hun to yo there
I'rum Clayton county. Charles 1'. Sheldon wa.s married in New \'ork,
and came Ironi there to Iowa about 1S34. In the .^l)rins.; of the
year followm- the close of the war .Mr. Shelilon came to Wn^ht
cotnity and .soon l)eL;an nnproNiny the ei-hty acres of land which
he ohtaiiied as a homestead. Here he lived nntil 187O, when he sold
the property and hons^ht an adjoining farm, where he lived until
ahout four years before the time of his death, which occurred on
I'ebruary j(\ niu. lie was a resielent of Dows the last four years of his
hfe. His devoted wife ]ias.ed away in l-"ebniaiy. k;!^. They were the
parents of live children as lollow : iMank IC, oi Williams, Iowa; Mrs.
.Memvill I'.n.tjle Km-, of Winnepe-, I aiiada ; Charles \., who lives in
Wisconsin: h". 1;., the subject of this sketch; ;md .Mrs. llattie
.McCoy, of Spooner, \\'isC(.)nsin. .\fter his schoolins^- was
completed — this consistin,^ of a tliorouj^h public-school tramino —
b'. li. Sheldon taii.^ht for nineteen terms and followed the plow
durinj4 summer vacations. L'litil his marriage he lued at home, and
after his marriage moved to a farm in X'ernon towiishi]) where he
li\ed until his reino\al to Kowan in ii)t)i. llere he Muceeded 1.. IC
Towers, who was at that time cashier of the Hank of Kowan, which
was a ])ri\ately owned banking institution, blight years later the
institution was iiicor|)orated as the State Saving.- Kank, and .Mr.
Slield..ii continued as its ca-hier. The hank was incorporated with a
capital of fifteen thousand dollars. The marriage cerem.my which
united in holy matrimony Ic li. Sheldon and his \vife occurred on
December _'4, iS()o, in this county. .Mrs. Sheldon being before this
event, lllanche Coulter, and was born in bVbruarv, iSjj, in (osh,.clon
county, Obi.i. She was the daughter of \. K. aiul Jennie ( oiilter,
n.itives r,i Ohio, they having come to Wright county about the year
>>\ 1SS3. One child has blessed this union, he being ( hi v K.
Sheldon who w.is born on June 3, iS(;j. lla\'ing graduated from the
local high scho,,l he later i^iaduated from the I'.ehiiond sebool lie
married I'.dna .Schroeder. Their only child, :\l;ixme, wa. born in
.March, i.,i5. Mr. Shekl.m is iifhliated with the Kepublican jKirtv and
although not an office seeker, has held a number (d' minor offices,
lie is a trustee of the MethodiM b'.piscopal church, of which his
family aKo are members. He is also trustee of the telephone
comi)any and of the school board. .\s cashier id' the bank he acts as
agent for sexeral insurance companies.
432 WKIGHT COUNTY, IOWA. Baiikiii. Sheldon. The
principles which ha\e been the gnide uf a strung, admirable
character, ha\e aLso been his guide in the commercial world in which
su much of his time and thought ha\e been spent. And, too, he has
never faikxl to lend his influence where it would efr'ect the general
good, and has supported tiio.se civic movements which e\er} jjublic-
spirited citizen endorses, thus attesting to his good citizenship.
Hb:XRV RURT From lingland have come to America many of her best
and most useful men, if we may judge of the character and life of
Henry Burt, the subject of this sketch. \ man of industrious ways,
intelligent in the use of his abilities, true to his determination to
succeed and one who made himself a worthy part of the nation of
his adoption, he is now one of the leading and most successful
farmers of the count)-. Henry bUu't was born in I'^ngland, thirty
miles from the city of Bristol, the son of William and Betsie Burt,
Ixjth of whom were natives uf iuiglantl. William Burt was a farmer of
his native country, a pursuit which he followed until his death in the
)-ear 1894. Betsie Burt sur\i\ed her husband and li\-es un the oU\
Burt home place in I'.ngland. William and lietsie liurt were the
parents of thirteen children, seven of whom are living, only tw(j of
whom li\e in the United States, Henry and a brother, James, wIkj li\-
es in Omaha, .\ebraska. Henry Burt, after receiving his education ii
worked until he was twenty years u\ age as a i America and lucated
in Trumbull countw Ohio, w and then moved t
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