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 PYTHON FOR
BIOINFORMATICS
SECOND EDITION
CHAPMAN & HALL/CRC
Mathematical and Computational Biology Series

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over the entire spectrum of mathematical and computational biology and
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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

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Department of Physics
University of Rome La Sapienza

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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:
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Applications Modeling Can Improve Cancer Therapy
Kiyoko F. Aoki-Kinoshita Outcomes
Computational Systems Biology of Vittorio Cristini, Eugene J. Koay,
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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
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Chromatin: Structure, Dynamics, Computational Neuroscience:
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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
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RNA-seq Data Analysis: A Practical Introduction to Bio-Ontologies
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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
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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
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Discovery Algorithms in Bioinformatics: A Practical
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and Epidemiology: Theory, Models, Introduction to Bioinformatics
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The Ten Most Wanted Solutions in
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Biology
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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
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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

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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
List of Tables

2.1 Arithmetic-Style Operators 26

3.1 Common List Operations 48

3.2 Methods Associated with Dictionaries 58

9.1 Sequence and Alignment Formats 175

9.2 Blast programs 178
9.3 eUtils 191

10.1 Frameworks for Web Development 233

12.1 Students in Python University 259

12.2 Table with primary key 260
12.3 MySQL Data Types 261

13.1 REGEX Special Sequences 287

A.1 Resources 367

xxi
Preface to the First Edition

This book is a result of the experience accumulated during several years of working
for an agricultural biotechnology company. As a genomic database curator, I gave
support to staff scientists with a broad range of bioinformatics needs. Some of them
just wanted to automate the same procedure they were already doing by hand, while
others would come to me with biological problems to ask if there were bioinformat-
ics solutions. Most cases had one thing in common: Programming knowledge was
necessary for finding a solution to the problem. The main purpose of this book is to
help those scientists who want to solve their biological problems by helping them
to understand the basics of programming. To this end, I have attempted to avoid
taking for granted any programming-related concepts. The chosen language for this
task is Python.
Python is an easy-to-learn computer language that is gaining traction among
scientists. This is likely because it is easy to use, yet powerful enough to accomplish
most programming goals. With Python the reader can start doing real programming
very quickly. Journals such as Computing in Science and Engineering, Briefings
in Bioinformatics, and PLOS Computational Biology have published introductory
articles about Python. Scientists are using Python for molecular visualization, ge-
nomic annotation, data manipulation, and countless other applications.
In the particular case of the life sciences, the development of Python has been
very important; the best exponent is the Biopython package. For this reason, Section
II is devoted to Biopython. Anyhow, I don’t claim that Biopython is the solution to
every biology problem in the world. Sometimes a simple custom-made solution may
better fit the problem at hand. There are other packages like BioNEB and CoreBio
that the reader may want to try.
The book begins from the very basic, with Section I (“Programming”), teaching
the reader the principles of programming. From the very beginning, I place a special
emphasis on practice, since I believe that programming is something that is best
learned by doing. That is why there are code fragments spread over the book. The
reader is expected to experiment with them, and attempt to internalize them. There
are also some spare comparisons with other languages; they are included only when
doing so enlightens the current topic. I believe that most language comparisons do
more harm than good when teaching a new language. They introduce information
that is incomprehensible and irrelevant for most readers.
In an attempt to keep the interest of the reader, most examples are somehow
related to biology. In spite of that, these examples can be followed even if the reader
doesn’t have any specific knowledge in that field.
To reinforce the practical nature of this book, and also to use as reference

xxiii
xxiv  Preface to the First Edition

material, Section IV is called “Python Recipes with Commented Source Code.”

These programs can be used as is, but are intended to be used as a basis for other
projects. Readers may find that some examples are very simple; they do their job
without too many bells and whistles. This is intentional. The main reason for this
is to illustrate a particular aspect of the application without distracting the reader
with unnecessary features, as well as to avoid discouraging the reader with complex
programs. There will always be time to add features and customizations once the
basics have been learned.
The title of Section III (“Advanced Topics”) may seem intimidating, but in
this case, advanced doesn’t necessarily mean difficult. Eventually, everyone will
use the chapters in this section [especially relational database management system
—RDBMS— and XML]. An important part of the bioinformatics work is building
and querying databases, which is why I consider knowing a RDBMS like MySQL
to be a relevant part of the bioinformatics skill set. Integrating data from different
sources is one of tasks most frequently performed in bioinformatics. The tool of
choice for this task is XML. This standard is becoming a widely used platform for
data interchange between applications. Python has several XML parsers and we
explain most of them in this book.
Appendix B, “Selected Papers,” provides introductory level papers on Python.
Although there is some overlapping of subjects, this was done to show several points
of view of the same subject.
Researchers are not the only ones for whom this book will be beneficial. It has
also been structured to be used as a university textbook. Students can use it for
programming classes, especially in the new bioinformatics majors.
Preface to the Second
Edition

The first edition of Python for Bioinformatics was written in 2008 and published
in 2009. Even after eight years, the lessons in this book are still valuable. This is
quite an accomplishment in a field that evolves at such a fast pace. In spite of its
usefulness, the book is showing its age and would greatly benefit from a second
edition.
The predominant Python version is 3.6, although Python 2.7 is still in use in
production systems. Since there are incompatibilities between these versions, lot of
effort was made to make all code in the book Python 3 compatible.
Not only has the software changed in these past eight years, but enterprise atti-
tude and support toward Open Source Software in general and Python in particular
has changed dramatically. There are also new computing paradigms that can’t be
ignored such as collaborative development and cloud computing.
In the original book, Chapter 14 was called “Collaborative Development: Version
Control” and was based on Bazaar, a software that follows the currently used
distributed development workflow but is not what is being used by most developers
today. By far the most software development is done with Git at GitHub. This
chapter was rewritten to focus on current practices.
Web development is another area that changed significantly. Although this is
not a book about web development, the chapter “Web Applications” now reflects
current usage of long-running processes and frameworks instead of CGI/WSGI and
middleware-based applications. Frameworks were discussed as a side note in this
chapter, but now the chapter is based around a framework (Bottle) and leave the
old method as a historical footnote.
In databases, the NoSQL gained lot of traction, from being a bullet point in
the first edition, now has its own section using MongoDB, and a Python recipe
was changed to use this NoSQL database.
Graphical libraries have improved since 2009, and there are great quality com-
peting graphic libraries available for Python. There is a whole chapter devoted to
Bokeh, a free interactive visualization library.
Another change that is reflected in this book is the usage of Anaconda and
Jupyter Notebooks (with all code in a cloud notebook provided by Microsoft
Azure1 ).
1
See https://notebooks.azure.com/py4bio/libraries/py3.us

xxv
xxvi  Preface to the Second Edition

Regarding source code, there is a GitHub repository at https://github.com/

Serulab/Py4Bio where you can download all the code and sample files used in this
book.
There are corrections in every chapter. Sometimes there were actual mistakes,
but most of the corrections were related to the Python 3 upgrade and in keeping
with current good practices. Regarding corrections, I expect that this book may
need corrections, so I made a web page where the readers can get updates. Please
take a look at http://py3.us and subscribe to the low volume mailing list while
at it.
Apart from software evolution and paradigms shifts, I also gained development
experience and changed my views on pedagogical matters. During these years I
worked in a genome sequencing project at an international consortium and as a
senior software developer in an NYSE listed company (Globant). In the last 5 years
I worked for several well-known clients such as Salesforce and National Geographic.
I am currently working at PLOS (Public Library of Science).
By request of MATLAB, I include their contact information:
MATLAB ® is a registered trademark of The MathWorks, Inc. For product
information please contact: The MathWorks, Inc. 3 Apple Hill Drive Natick, MA,
01760-2098 USA Tel: 508-647-7000 Fax: 508-647-7001 E-mail: info@mathworks.com
Web: www.mathworks.com
Regarding the logo of Biopython, that is used in the cover, here it is usage
license (this covers all Biopython files, including its logo):
Biopython is currently released under the "Biopython License Agreement"
(given in full below). Unless stated otherwise in individual file headers, all Biopy-
thon’s files are under the "Biopython License Agreement".
Some files are explicitly dual licensed under your choice of the "Biopython Li-
cense Agreement" or the "BSD 3-Clause License" (both given in full below). This
is with the intention of later offering all of Biopython under this dual licensing
approach.

Biopython License Agreement

Permission to use, copy, modify, and distribute this software and its documenta-
tion with or without modifications and for any purpose and without fee is hereby
granted, provided that any copyright notices appear in all copies and that both
those copyright notices and this permission notice appear in supporting documen-
tation, and that the names of the contributors or copyright holders not be used in
advertising or publicity pertaining to distribution of the software without specific
prior permission.
THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFT-
WARE DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFT-
WARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY
AND FITNESS, IN NO EVENT SHALL THE CONTRIBUTORS OR COPY-
RIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT OR CON-
SEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING
 Preface to the Second Edition  xxvii

FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF

CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT
OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS
SOFTWARE.

BSD 3-Clause License

Copyright (c) 1999-2017, The Biopython Contributors All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
Redistributions of source code must retain the above copyright notice, this list of
conditions and the following disclaimer. Redistributions in binary form must repro-
duce the above copyright notice, this list of conditions and the following disclaimer
in the documentation and/or other materials provided with the distribution. Nei-
ther the name of the copyright holder nor the names of its contributors may be
used to endorse or promote products derived from this software without specific
prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPY-
RIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR
IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IM-
PLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PAR-
TICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPY-
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RECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAM-
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CLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF
THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY
OF SUCH DAMAGE.
Discovering Diverse Content Through
Random Scribd Documents
Every generation has its own “religious difficulty,” by which phrase is
meant, not the difficulty which the individual soul or the collective
soul of a nation may find in its religious beliefs themselves, but a
difficulty which intrudes itself into allied or alien matters from the
sphere of religious disputation. In the present day, the religious
difficulty with which we are most familiar concerns questions of
education. In the days of Miss Nightingale's mission to the East there
was a religious difficulty in questions of nursing.

It was not enough that such a mission as hers was conceived in

the very spirit of the Founder of Christianity: “I was sick, and ye
visited me.” The question was eagerly and angrily canvassed under
which of the rival Christian banners the visitation of the sick soldiers
should be, and was being, carried on. The country had at the time
hardly recovered its mental equilibrium after the shock administered
to it by the Tractarian movement, and echoes of the “No Popery” cry
of 1850 were still resonant in many quarters. The religious difficulty
appeared at the very start of Miss Nightingale's Crimean work, and
dogged her footsteps to the end of it. I have dealt already with the
difficulties which her experiment encountered from social ideas,
military prejudices, official routine; but I am not sure that of all her
difficulties the religious one was not the most wearing and worrying,
as it was also assuredly the most unnecessary and the least
excusable. It enveloped a noble undertaking in a fog of envy, strife,
and futile railing.

Mr. Sidney Herbert, who was supposed to be of the High Church

persuasion, had scented the difficulty from the first, as we have
heard, and Miss Nightingale was keenly alive to it. They had desired
to make the first party of nurses representative of all the leading
sects; but owing to the abstention of a Protestant institution, the
Roman Catholics and the High Church party were in a considerable
majority among the thirty-eight nurses. This fact gave the alarm,
and a sectarian hue-and-cry was immediately raised. It began, as I
am sorry to have to say, in the Daily News; it was taken up, as goes
without saying, in the so-called “religious press.” On October 28,
1854, when Miss Nightingale was on her way to Scutari, an attack
upon her was given great prominence in the first-named paper. It
was signed “Anti-Puseyite,” and it included the text of Mr. Herbert's
letter which had somehow or other been obtained.[161] “Miss
Nightingale recruited her staff of nurses from Miss Sellon's house [a
High Church one] and from a Romanist establishment.” This awful
fact explained “the party spirit which actuated the choice of Miss
Nightingale for this important and responsible office, and which set
aside Lady Maria Forester”—a lady, it seems, of Evangelical
principles. It was not yet too late to remedy the offence “if the
feeling of the nation be at once aroused and expressed.” “A Reader
of the Bible” and other correspondents followed, and the controversy
raged furiously. Mrs. Sidney Herbert's intervention, with an
assurance that Miss Nightingale was somewhat Low Church, did not
stop it. S. G. O. referred to it in his book. “I have heard and read,”
he wrote, “with indignation the remarks hazarded upon her religious
character. Her works ought to answer for her faith. If there is blame
in looking for a Roman Catholic priest to attend a dying Romanist, let
me share it with her—I did it again and again.”[162] An admirable
avowal, but not calculated, I fear, to allay the anger of “No Popery”
fanatics. The publication of Queen Victoria's letter of December 6
(p. 215), showing the confidence which Her Majesty placed in Miss
Nightingale, did something to stem the tide, but for many months
the feud flowed on in the press.

II

Miss Nightingale's comment, when echoes of the storm reached

her on the Bosphorus, was characteristic. “They tell me,” she wrote
to Mr. Herbert (Jan. 28, 1855), “that there is a religious war about
poor me in the Times, and that Mrs. Herbert has generously
defended me. I do not know what I have done to be so dragged
before the Public. But I am so glad that my God is not the God of
the High Church or of the Low, that He is not a Romanist or an
Anglican—or a Unitarian. I don't believe He is even a Russian,
though His events go strangely against us. (N.B.—A Greek once said
to me at Salamis, ‘I do believe God Almighty is an Englishman.’)”
Excellent, too, was the answer given by an Irish clergyman when
asked to what sect Miss Nightingale belonged. “She belongs to a
sect which, unfortunately, is a very rare one—the sect of the Good
Samaritan.” Miss Nightingale was by descent a Unitarian, by practice
a communicant of the Church of England; but she was addicted
neither to High Church nor to Low. Her God was the God of Moral
Law, a God of infinite pity and benevolence, but also One who
worked out His purpose by the free will of human instruments. Her
service of God was the service of Man, and her service of Man
mingled efficiency with tenderness. She applied only one kind of test
to a nurse: Was she a good woman, and did she know her business?
To be a good woman, a religious woman, a noble woman was not in
itself sufficient. “Excellent, gentle, self-devoted women,” Miss
Nightingale said in a note upon some of her staff, “fit more for
Heaven than for a Hospital, they flit about like angels without hands
among the patients, and soothe their souls, while they leave their
bodies dirty and neglected. They never complain, they are eager for
self-mortification. But I came not to mortify the nurses, but to nurse
the wounded.” Therefore if a nurse was a good woman and knew
her business, it was nothing that she was Romanist, Anglican, High
Church, Low Church, or Unitarian. If she was not a good nurse, the
fact that she belonged, or did not belong, to this or that persuasion
was no recommendation. Miss Nightingale was, it is true, desirous
from the first to include Roman Catholics in her staff, and she did so,
in spite of many difficulties, to the end. But her reasons therein were
practical, not sectarian. In the first place, many of the soldiers were
Roman Catholics; and, secondly, her apprenticeship in nursing had
shown her the excellent qualities, as nurses, of many Catholic
Sisters. But here efficiency was the test, and a Protestant Deaconess
from Kaiserswerth was all one to her with a Sister from “a Romanist
establishment.” And one practical advantage of vowed Sisters was
that she did not lose them from marriage. One morning six nurses
came in to Miss Nightingale, declaring that they one and all wished
to be married. They were followed by six soldiers—sergeants and
corporals—declaring their desire to claim the nurses as brides. This
matrimonial deluge carried off six of her best nurses.[163]

III

Such, then, was Miss Nightingale's position; and one can

understand the amused contempt with which she heard of the
picture drawn of her in certain quarters as a conspirator in a
Tractarian or Romanist plot. But she was a practical person, and,
though herself broad-minded, took stock of a narrower world as she
found it. She was intensely desirous of making her experiment of
woman nurses a success, and she felt acutely the danger of
wrecking it by even the suspicion of sectarian prejudice. This fact
supplies a further explanation of the alarm with which she received
the coming of the second party of nurses under Miss Stanley.[164] It
included a batch of fifteen nuns. “The proportion of R. Catholics,”
she wrote to Mr. Herbert, “which is already making an outcry, you
have increased to 25 in 84. Mr. Menzies [the Principal Medical
Officer] has declared that he will have two only at the General
Hospital, and I cannot place them here [in the Barrack Hospital] in a
greater proportion than I have done, without exciting the suspicion
of the Medical Men and others.” The difficulty was ultimately
adjusted, but only at the cost of infinite trouble and worry to Miss
Nightingale. Her letters to Mr. Herbert are full of references to the
subject, some of them very amusing, and perhaps it was her lively
sense of humour that helped to carry her through this religious
difficulty. “Such a tempest,” she wrote (Dec. 25, 1854), “has been
brewed in this little pint pot as you could have no idea of. But I, like
the Ass, have put on the Lion's skin, and when once I have done
that (poor me, who never affronted any one before), I can bray so
loud that I shall be heard, I am afraid, as far as England. However,
this is no place for lions; and as for asses, we have enough.” One
proposition made to her was that, as the doctors did not want many
more woman nurses, “ten of the Protestants should be appropriated
as clerical females by the chaplains, and ten of the nuns by the
priests, not as nurses, but as female ecclesiastics. With this of
course I have nothing to do. It being directly at variance with my
instructions, I cannot of course appropriate the Government money
to such a purpose.” Miss Nightingale's own proposition was to
allocate the party in various proportions to various hospitals; but the
Superior of the new set of nuns objected that “it would be
uncanonical” for any of her party to be separated from her. Then
Miss Nightingale proposed sending some of the nuns, either of the
first or of the second batch, back to England; but Father Cuffe said
that to send them away would be “like the driving of the Blessed
Virgin through the desert by Herod.” “I believe it may be proved as a
logical proposition,” wrote Miss Nightingale in the midst of her
religious difficulty, “that it is impossible for me to ride through all
this; my caique is upset, but I am sticking on the bottom still.” Three
days later she still despaired. “The fifteen New Nuns are leading me
the devil of a life, trying to get in vi et armis, and will upset the
coach; there is little doubt of that.” However, she held her ground.
She had started with a Protestant howl at her; she was now
prepared to face “a Roman Catholic storm.” Happily the Reverend
Mother of the first party of nuns was on her side, and strove to
compose the canonical difficulty. To another Reverend Mother, who
was less peaceably minded, Miss Nightingale often referred in her
letters as “the Reverend Brickbat.” In any case, Miss Nightingale was
resolved, as she wrote, “not to let our little Society become a hot-
bed of Roman Catholic Intriguettes.” Ultimately it was arranged that
five of the second party of nuns should go to the General Hospital,
and ten to the newly opened hospital at Koulali. Miss Nightingale
suspected some of the second party of a desire to proselytize; and
presently she had to inform Mr. Herbert (Feb. 15, 1855) of “a charge
of converting and rebaptizing before death, reported to me by the
Senior Chaplain, by him to the Commandant, by him to the
Commander-in-Chief.” She promptly exchanged the suspected nun.

The ingenuity of theological rancour was infinite. Having caught

wind of the fact that there was some difference of view among the
Roman Catholic Sisters, an Evangelical writer sought to fan the flame
by denouncing the absurdity of “Catholic Nuns transferring their
allegiance from the Pope of Rome to a Protestant Lady.” One of the
Sisters, on hearing of this diatribe, playfully addressed Miss
Nightingale as “Your Holiness,” who in turn dubbed the Sister “her
Cardinal.”[165] I hereby give notice, in case Crimean letters from Miss
Nightingale should chance to be printed (such as I have seen) in
which she says, “I do so want my Cardinal,” that the expression
signifies no dark and secret adhesion to any Prince of the Roman
Church, but only a desire for the services of a particularly efficient
nursing Sister. If a nurse was efficient, Miss Nightingale was on the
friendliest terms with her, equally whether the nurse were Catholic
or Protestant. Miss Nightingale herself was accused successively, and
with equal absurdity in each case, of being prejudiced for, or against,
Catholics and Protestants, and of being inimical to religious
ministrations altogether.[166] The Protestant charges of proselytizing
by Catholic nurses were of course met by counter-charges of
attempts by Protestant nurses to convert Roman Catholic patients;
and finally a chaplain solemnly appealed to the War Department in
London to remove one of Miss Nightingale's staff on the ground that
the nurse had been heard to avow herself a Socinian. Miss
Nightingale protested successfully against any such disciplinary
measure, urging that the lady, whether Socinian or not, was an
excellent nurse. Much of all this perverse disputing was born of
sheer ignorance and intolerance. One of Miss Stanley's ladies was
accused by a certain chaplain of “circulating improper books in the
wards.” Particulars were asked, and it was found that the offending
book was Keble's Christian Year.[167]

No sooner was any one phase of the religious difficulty adjusted

than another appeared. There were Anglicans and Roman Catholics
among the Nightingale nurses, and there were others selected from
English hospitals, who, so far as their religious views were
concerned, might be anything or nothing. But why, it was asked,
were there no Presbyterians? Representations were made to the War
Office. “I object,” wrote Miss Nightingale (Feb. 19, 1855), “to the
principle of sending out any one, qua sectarian, not qua nurse. But
this having already been done in the case of the R.C.'s, etc., I do not
see how the Presbyterians can be refused. And therefore let six
trained nurses be sent out, if you think fit, of whom let two-thirds be
Presbyterians. But I must bar these fat drunken old dames. Above
14 stone we will not have; the provision of bedsteads is not strong
enough. Three were nearly swamped in a caique, whom
Mr. Bracebridge was conducting to the ship, and, had he not walked
with the fear of the police before his eyes, he might easily have
swamped them whole.” The stout old dames were not Presbyterians;
but, sad to relate, two of the Presbyterian party did turn out to be
over-fond of drink, and Miss Nightingale had to return them to
England. I regret to say that there were similar cases, not amongst
the Presbyterians.

The charges and counter-charges of proselytism were referred by

the chaplains to the Secretary of State. Lord Panmure, in reply (April
27, 1855), had “to say in the first place, that he has perused the
correspondence with great regret, and that he deeply laments to
find that religious differences have arisen to such an extent as to
mar the united energies and labours of those who are devoting
themselves with such disinterestedness and heroic courage and
success to the relief of the sick and wounded.” The Minister then
proceeded to promulgate instructions designed to prevent any
proselytism by the nurses and Sisters. Unfortunately, his dispatch
was so worded as to make things, from Miss Nightingale's point of
view, no better, but rather worse. “The instructions,” she wrote to
Lady Canning (Sept. 9, 1855), “have been so completely
misunderstood that they have been my principal difficulty. The R.C.'s
who before were quite amenable have chosen to construe the rule
that they ‘are not to enter upon the discussion of religious subjects
with any patients other than those of their own faith,’ to mean
therefore with all of their own faith, and the second party of nuns
who came out now wander over the whole Hospital out of nursing
hours, not confining themselves to their own wards, nor even to
patients, but ‘instructing’ (it is their own word) groups of Orderlies
and Convalescents in the corridors, doing the work each of ten
chaplains, and bringing ridicule upon the whole thing, while they
quote the words of the War Office.” Lady Canning, who was at this
time acting as Miss Nightingale's agent for the enlistment of nurses,
had proposed to embody Lord Panmure's instructions in the printed
Rules and Regulations. Miss Nightingale begged her to do no such
thing. I doubt not that Miss Nightingale's own verbal instructions
were less ambiguous. She was one who never failed to say exactly
what she meant.

IV

A great obstacle with which Miss Nightingale's work in the East

had to contend throughout was the scarcity at the time of properly
trained nurses. She had long ago formed a resolve to remedy this
defect; the seriousness of it was still further enforced upon her mind
by painful experience in the Crimean War; and her resolve was the
more strengthened. The religious difficulty—demanding that nurses
should be selected, to some extent, not qua nurses, but qua
sectarians—accentuated the obstacle of inadequate training, which,
however, would in any case have existed. The case is excellently put,
in terms which doubtless reflect Miss Nightingale's own views, in a
letter from Lady Verney to Mrs. Gaskell (May 17, 1855):—
 Until women have gone through a real training, it is vain to hope that
four or five weeks in a Hospital can fit them for one of the most difficult
works that any one can be called on to undertake. I cannot tell you the
details, you can guess many of them; but when I hear estimable people
talking as if you could turn 40 women of all ranks, degrees of virtue, and
intelligence, into a Military Hospital, with drunken orderlies, unmarried
Chaplains, young Surgeons, &c., &c., and expect that they are not more
likely to be unwise or tempted astray than the R.C. Sisters of Charity, who
are bound by well-considered vows, love of their kind and the fear of Hell
fire, then we feel that the “estimable people” have very little knowledge of
human nature. F.'s form of Sisterhood is infinitely higher, I believe, than
the R.C. and will be carried out, I doubt no more than in her own
existence, but as it must exist without the checks and safeguards of the
other and inferior form, so it requires higher elements in the actors and a
more severe training and examination. Instead of which the loosest
possible choice takes place by people most excellent but not in the least
qualified to choose; goodwill and a “love of nursing” is enough for the
Lady class.

It is the fact, though it is not popularly known, that Miss

Nightingale was at this time strongly opposed to “lady” nurses. She
objected to them, not because they were ladies, but because they
were unlikely to be well trained. Pious and benevolent ladies were
more given, she said, to “spiritual flirtations with the patients,” than
apt at the proper business of surgical nursing. It was the trained
hospital nurses that she preferred. There were among the 125
women who passed through her hands in the East more efficient
and less, and in so large a flock there were some black sheep. But
amongst the band, in all classes and of all denominations, there
were devoted and competent women, whose services deserve to be
held in grateful remembrance beside those of their Lady-in-Chief.
And as I have had to record Miss Nightingale's criticism upon some
of the Roman Catholics among her flock, it should be added that of
others she wrote to Mr. Herbert: “They are the truest Christians I
ever met with—invaluable in their work—devoted, heart and head, to
serve God and mankind—not to intrigue for their Church.” To the
Reverend Superior, who came out from Bermondsey with the first
party of nuns, Miss Nightingale was particularly attached. “She
writes,” said Cardinal Wiseman, “that great part of her success is due
to Rev. Mother of Bermondsey, without whom it would have been a
failure.”[168]

The aspect of Miss Nightingale's work, touched upon in this

chapter, adds another to the accumulation of difficulties with which
she had to deal. It was the one which troubled her most. “In this
sink of misery, in this tussle of life or death,” she felt the bitter futility
of personal grievances and religious differences. It is worry, more
than work, that kills; and the religious difficulty was perhaps the last
straw which caused the Lady-in-Chief to break down, as we shall
hear in the next chapter, under her heavy load of responsibility and
care.

CHAPTER IX

TO THE CRIMEA—ILLNESS
(May–August 1855)

For myself, I have done my duty. I have identified my fate with that of
the heroic dead.—Florence Nightingale (private notes, 1855).

In the spring of 1855 Miss Nightingale decided to leave Scutari for a

while in order to visit the hospitals in the Crimea. The conditions at
Scutari were now greatly improved. Sanitary works had been
executed. The hospitals were better supplied. The pressure in the
wards, caused by the terrible winter before Sebastopol, was relieved.
There were only 1100 cases in the Barrack Hospital, and of those
only 100 were in bed. The rate of mortality had fallen from 42 per
cent to 22 per thousand of the cases treated. The siege was likely
soon to be accompanied by assaults, and the pressure might rather
be in the hospitals at Balaclava, where the sick and wounded were if
possible to remain, in order to avoid the sufferings of the sea
passage to Scutari.

In the Crimea, besides the regimental hospitals, there were four

general hospitals. There was the General Hospital at Balaclava,
established after the British occupation in September 1854. There
was the Castle Hospital, consisting of huts on the “Genoese heights”
above Balaclava, opened in April 1855. There was the Hospital of St.
George's Monastery, also consisting of huts, intended for
convalescent and ophthalmic cases; and, lastly, there were the
Hospitals of the Land Transport Corps, again consisting of huts, near
Karani. All these hospitals had a complement of female nurses,
though the Monastery Hospital not until December 1855, and the
Land Transport Hospitals not until 1856. In the spring of 1855, then,
there were already female nurses at the General Hospital and the
Castle Hospital, under their own superintendents, but all ultimately
responsible to Miss Nightingale—as she apprehended, and as the
War Office intended. She was now anxious to inspect these
hospitals; to increase the efficiency of the female nursing
establishments; and, in particular, to introduce those washing and
cooking arrangements which had been productive of so much
benefit at Scutari. Her visit of inspection was approved by the War
Office; and, by instructions dated April 27, she was invested with full
authority as Almoner of the Free Gifts in all the British Hospitals in
the Crimea. But in other respects her position was somewhat
ambiguous. The original instructions, issued by Mr. Herbert, had
named her as Superintendent of the female nurses in all the British
military hospitals in Turkey; and these words gave a standing-ground
to her opponents in the Crimea. The intention of the War Office was
to give her general superintendence, but to relieve her of direct
responsibility for the nurses in the Crimea so long as she was at
Scutari. The matter was not, however, cleared up till a later date,
[169] and the indefiniteness of her position in the Crimea exposed
her to infinite worry and intrigues.

On May 2, Miss Nightingale set forth from Scutari, where

Mrs. Bracebridge was left in charge:—
“Poor old Flo,” Miss Nightingale wrote from the Black Sea, May 5, 1855,
“steaming up the Bosphorus and across the Black Sea with four nurses,
two cooks, and a boy to Crim Tartary (to overhaul the Regimental
Hospitals) in the Robert Lowe or Robert Slow (for an exceedingly slow
boat she is), taking back 420 of her patients, a draught of convalescents
returning to their regiments to be shot at again. ‘A Mother in Israel,’ Pastor
Fliedner called me; a Mother in the Coldstreams, is the more appropriate
appellation. What suggestions do the above ideas make to you in Embley
drawing-room? Stranger ones perhaps than to me, who, on the 5th May,
year of disgrace 1855, having been at Scutari six months to-day, am in
sympathy with God, fulfilling the purpose I came into the world for. What
the[256] disappointments of the conclusion of these six months are no one
can tell. But I am not dead, but alive.”

Miss Nightingale was accompanied to the Crimea by the faithful

Mr. Bracebridge, willing as ever to serve her. Among the nurses was
Mrs. Roberts, whose exceptional efficiency and personal devotion to
the Lady-in-Chief were soon to be called in need. Of the cooks, the
chief was Soyer the Great, from whose cheerfully gossiping and
pleasantly egotistical pages[170] some details are drawn in this
chapter. The “boy” mentioned in Miss Nightingale's letter was
Thomas, a drummer, who, though only twelve years of age, used to
call himself “Miss Nightingale's Man.” He was a regular enfant de
troupe, says M. Soyer, full of activity, wit, intelligence, and glee. He
would draw himself up to his full height, and explain that he had
“forsaken his instruments in order to devote his civil and military
career to Miss Nightingale.” She was attended also by a soldier
invalided from the 68th Light Infantry, whom Mr. Bracebridge had
picked out to serve as messenger. In 1860 he wrote a manuscript
account of his experiences in the Crimea,[171] and this is another
first-hand source from which particulars are drawn in the present
chapter. The party arrived at Balaclava on May 5, and the decks of
vessels in the harbour were crowded with spectators anxious to
catch a glimpse of the famous Lady-in-Chief. There was no
accommodation for her ashore; so her headquarters were on board
the Robert Lowe, and when that vessel left, on the sailing transport
London.

II

Miss Nightingale set to work immediately, and with characteristic

energy. One of her first duties was a visit of ceremony to Lord
Raglan. She was a good horsewoman, and as a girl had been fond of
riding. She was now mounted “upon a very pretty mare, which, by
its gambols and caracoling, seemed proud to carry its noble charge,
and our cavalcade produced an extraordinary effect upon the motley
crowd of all nations assembled at Balaclava, who were astonished at
seeing a lady so well escorted.” Was not the great Soyer himself
among the escort? The Commander of the Forces was away, but
Miss Nightingale was taken to the Three Mortar Battery, and the
soldiers, as she passed, gave her three times three. This visit to the
front made a profound and indelible impression upon her.[172] It is
first recorded in a letter of May 10, which was forwarded to Windsor
Castle.[173] “Fancy,” she wrote, “working five nights out of seven in
the trenches! Fancy being 36 hours in them at a stretch, as they
were all December, lying down, or half lying down, often 48 hours
with no food but raw salt pork, sprinkled with sugar, rum, and
biscuit; nothing hot, because the exhausted soldier could not collect
his own fuel, as he was expected to do, to cook his own ration; and
fancy through all this the army preserving their courage and
patience as they have done, and being now eager (the old ones
more than the young ones) to be led even into the trenches. There
was something sublime in the spectacle.” “When I see the camp,”
she wrote to Lady Canning (May 10), “I wonder not that the army
suffered so much, but that there is any army left at all; but now all is
looking up. Sir John M'Neill has done wonders.” With Sir John M'Neill,
a doctor who afterwards entered the Political Service in the East,
Miss Nightingale formed a great friendship. He, with Colonel Tulloch,
had been sent out to the Crimea by Lord Palmerston's Government
to report upon the Commissariat system.

Miss Nightingale, on this and her later visits to the Crimea, saw
and heard of many deeds of heroism which she loved to tell. “I
remember,” she wrote, “a sergeant, who was on picket, the rest of
the picket killed, and himself battered about the head, stumbled
back to camp, and on his way picked up a wounded man, and
brought him in on his shoulders to the lines, where he fell down
insensible. When, after many hours, he recovered his senses, I
believe after trepanning, his first words were to ask after his
comrade, ‘Is he alive?’ ‘Comrade, indeed! yes, he's alive, it is the
General.’ At that moment the General, though badly wounded,
appeared at the bedside. ‘Oh, General, it's you, is it, I brought in,
I'm so glad. I didn't know your honour, but if I'd known it was you,
I'd have saved you all the same.’ This is the true soldier's spirit.”[174]

III

During the few days immediately after her arrival at Balaclava,

Miss Nightingale carried on an active investigation of the hospitals,
regimental and general; arranged various affairs in connection with
the sisters and nurses; discussed the building of new huts; and, in
conjunction with M. Soyer, planned the erection of several kitchens
for extra diet. Here, as at Scutari, she was fearless of contagion, and
tended patients stricken with fever. On return to her ship one
evening she complained of great fatigue; and on the following
morning, feeling no better, she sent for Dr. Anderson, Chief Medical
Officer at the General Hospital. He called others of the medical staff
into consultation, and a joint bulletin was issued to the effect that
Miss Nightingale was suffering from Crimean fever. They advised that
she should be removed from the ship, and she was carried on a
stretcher by relays of soldiers to the Castle Hospital on the Genoese
Heights. The hut in which she lay was immediately behind those of
the wounded soldiers. The attack of fever was sharp, and she was,
as she afterwards admitted to her friends, “very near to death.”
There are scraps of manuscript among her papers (for even in illness
she could not be kept from the use of her pen) which show a
wandering mind.

The news of Miss Nightingale's illness was received with

consternation in England, and the anxiety of her friends was intense,
though Lord Raglan had thoughtfully arranged that a telegraphic
dispatch from him should not reach them till, after two or three days
of the fever, the doctors were able to hold out hopes of recovery.
“Sitting to-day,” wrote her sister to a friend, from Embley (May 27),
“in the little Vicarage woodhouse, waiting for the people to come out
from church (for we were not up to the whole service), in order to
go in to the Communion which she loves so well, and which we
always take with her and God, and which she is taking in spirit or
reality to-day if she is alive, and if not is taking in a higher and
happier sense—Mama said, 'I thank God she is ready for life or for
death'; and in that, dear, we truly strive to rest, though the spirit
would quail, I am afraid, if there were not hope at the bottom.” The
anxiety in the War Hospitals was scarcely less. “The soldiers turned
their faces to the wall,” said one, “and cried.” The crisis passed, and
on May 24 Lord Raglan was able to telegraph home that the patient
was out of danger, and three days later that she was going on
favourably. The bulletins were forwarded to the Queen, and on May
28 Her Majesty, in writing to Lord Panmure, was “truly thankful to
learn that excellent and valuable person, Miss Nightingale, is
safe.”[175] At this time a horseman rode up to her hut, and the
nurse, Mrs. Roberts, who had been enjoined to keep the patient
quiet, refused to let him in. He said that he most particularly desired
to see Miss Nightingale. “And pray,” said Mrs. Roberts, “who are
you?” “Ah, only a soldier,” replied the visitor, “but I have ridden a
long way, and your patient knows me very well.” He was admitted,
and a month later was himself laid low and died. It was Lord Raglan.

IV

Miss Nightingale, on becoming convalescent, was strongly advised

by the doctors to take a voyage to England. She would not listen to
such advice. Her work at the front had but just begun, and she was
resolved to return to it after the shortest possible delay. The voyage
to the Bosphorus was the longest that she could be induced to take.
Her good Mrs. Bracebridge had arrived from Scutari just in time to
accompany her friend on the return voyage. Lord Ward, whose
steam-yacht was in harbour at the time, pressed the use of it upon
her, and in it she was taken to Scutari. When the yacht reached
Scutari, all the high officials were present to meet it. One of the
large barges, used to remove the sick and wounded, was brought
alongside, and Miss Nightingale, in a state of extreme weakness and
exhaustion, was lowered into it. At the pier soldiers were in
readiness, who carried her on a stretcher to the chaplain's house,
followed by a large and sympathetic crowd. “I do not remember
anything during the campaign,” wrote the good-hearted Soyer, “so
gratifying to the feelings as that simple though grand procession.”
“Ah,” said a soldier, “there was no sadder sight than to see that dear
lady carried up from the pier on a stretcher just like we men, and
perhaps by some of the fellows she nursed herself.”[176] It was the
same when she was presently moved from Scutari to the shore in
order to go to Therapia, where the Ambassador had placed his
summer residence at her disposal. She was carried in a litter by four
guardsmen, but, though it was only five minutes' walk to the shore,
there were two relays, and her baggage was divided among twelve
soldiers, though two could easily have carried the whole,[177] so
great was the desire of the men to share in the honour of helping
the Lady-in-Chief.

Her recovery was gradual, and her weakness great. Mrs.

Bracebridge described her as unable to feed herself or speak above
a whisper. The extreme exhaustion was more from the previous
overstrain on mind and body than from the fever, the doctors said,
and they recommended complete change and rest. Mr. Sidney
Herbert wrote, imploring her to come home for two months: “We are
delighted,” wrote her mother (July 9), “to think of you at Therapia.
Oh, my love, how I trust that you will, among the numerous lessons
which your life has been spent in learning, be able to perfect that
most difficult one of standing and waiting.” She was to be lessoned
in that form of service, but not till after many more years of arduous
labour, and for the present she would not hear of any return to
England. The feeling of the soldiers for her touched her so deeply
that she could not bear, she said, to leave them. Gradually she
recovered strength. “We have a charming account,” wrote her sister
(Aug. 21), “from Lothian Nicholson just ordered out to Crimea, who
is quite enthusiastic, dear old boy, about her good looks, which, as
all her hair has been cut off, is good testimony—‘her own smile,’ he
talks of, and says he can hardly believe she has gone through such a
winter. The dear Bracebridges say that her improvement in the last
week was delightful and wonderful.” Already, in July, her business
letters were resumed. In August she was in the full rush of work
again. The doctors and her friends still besought her to take rest.
But her indomitable spirit would listen to no counsels of retreat. The
end of the war was not yet in sight. Even Sebastopol had not yet
fallen. So long as there remained sick and wounded in the Levant to
be cared for, she was resolved to remain also. A soldier was told that
the Lady-in-Chief would probably be sent home. “But how will they
pairt with her,” he said, “what'll they do without her? they set all
their hopes on she.” There were nurses, too, naturally anxious to
rejoin their families or friends at home, who said that, if she went,
they would go. The presence of Miss Nightingale, with her lofty
ideals and inspiring self-devotion, was the attraction which kept
many of these women at their posts. Some had already died.
Mrs. Elizabeth Drake, one of the nurses whom Miss Nightingale had
taken with her to the Crimea, died on August 9 of low fever at
Balaclava. “I cannot tell you,” wrote Miss Nightingale to the Master
of St. John's House (Aug. 16, 1855), “what I felt when I heard of her
death, unexpected alike by all. Her two physicians thought her going
on well, and I expected her in every convoy that came down from
Balaclava, as she was coming to me to recruit. I have lost in her the
best of all the women here. Once I proposed to her to go home, but
she scouted the idea entirely and said her health was better here
than in England. I feel like a criminal in having robbed you of one so
truly to be loved and honoured. It seemed as if it pleased God to
remove from the work those who have been most useful to it. His
will be done!” Nurse Drake's body was brought to Scutari, and Miss
Nightingale erected a small marble cross over it in the cemetery. It
was no time, when members of the rank-and-file were falling at the
post of duty, for the chief to listen to counsels of medical prudence.
Nor, indeed, at any time did Miss Nightingale harbour even a passing
thought of what would have seemed to her an act of military
desertion. She remained till the end of the war came, and till the last
transport had sailed; working indefatigably as ever, and in some
respects in new spheres of usefulness, both in the Crimea and at
Scutari; to what good effect we shall hear in later chapters, but at
great cost to her own comfort and bodily strength. She had been
appointed, as she used to say, to a subsidiary post in the Queen's
Army[178]; the humblest post, it might be, but still a post of duty.
The men had dared and suffered; and Florence Nightingale was
resolved to show that a woman too had strength to suffer and
endure.
 During the weeks of convalescence at Scutari, Miss Nightingale
used sometimes to walk at evening on the shore, in full sight of that
view which, when she had first come there, they told her was the
finest in the world, but which, in the crush of work, she had no time
to enjoy.[179] She sent a letter to her people at home describing one
such evening walk, and it was read out in the family circle. Lady
Byron, who was staying with them at the time, heard it read, and
said that it was “like a hymn—simple and deep-toned.” She
described how, on the opposite side, the city of Constantinople was
defined against the burning sky of the setting sun, but the outline
was changed by the fall of some mounds in an earthquake. Near her
were the graves of the heroic dead, the thousands with whom, she
said, she felt identified. “It went into my heart,” wrote Lady Byron,
“as the poetry of fact—for she has made poetry fact.” The letter
went on to speak of the British burying-ground at Scutari, and Miss
Nightingale added these lines:—
“They are not here!” No, not beneath that sod,
And yet not far away,
For they can mingle their new life from God
With living souls, not clay.

And they, “the heroic dead,” will softly pour

Into thy spirit's ear
A music human still, but sad no more,
To tell thee they are near—

Near thee with higher ministering aid

Thy heart-work to return,
So that each sacrifice that love has made
A victory shall earn![180]
 CHAPTER X

THE POPULAR HEROINE

Miss Nightingale looks to her reward from this country in having a fresh
field for her labours, and means of extending the good that she has
already begun. A compliment cannot be paid dearer to her heart than in
giving her work to do.—Sidney Herbert.

The news of Miss Nightingale's illness spread sympathetic anxiety

throughout Great Britain. Even more than when her mission of
mercy was first announced, she became the popular heroine; and
more than ever men and women of all classes sought means of
showing their sympathy.

Lady Verney, whose depth of feeling is not concealed by the play

of humour which sparkles pleasantly upon the surface, described,
successively, the penalties and the pleasures of being the sister of a
heroine:—

(Miss F. P. Nightingale to Miss Ellen Tollet.) Embley, Friday [Summer of

1855]. I am quite done with writing, a second blast of linen and knitted
socks was nearly the death of me, and ‘hints,’ my dear!—oh, my horror of
being asked for hints,—such as “can newspapers be put into the post
free?” and such like niaiseries. How grateful I am to you for never once
having inquired whether socks or muffetees are most required, and
whether you are safe in sending 6 towels and an old tablecloth to London,
or whether they had better come to us. It sounds very ungrateful, I am
afraid, but when one's wrist aches over the two hundredth repetition of
the matter, I do wish the public would apply to the nearest post office, or
read that scarce and erudite work the Times, and use their sense not their
pens.

However, these words are only when I am cross at having been

prevented from writing to the folk I love, such as thee, of the progress of
Scutari. Else generally the feeling in every soul, so wide and so deep,
touches us more than I can tell, and helps us over the inevitable weight of
the anxiety more than I thought[265] possible—heavy, redfaced, old fox-
hunting Squires, who never had a “sentiment” in their lives, come with
their eyes full of tears; narrow-minded Farmers with both eyes on the
main chance are melted; young ladies who never got beyond balls and
concerts are warmed. Dearest, I do feel of the feeling she has raised, it
blesseth “him here who gives and those out there who take,” and will do
good wider than one hoped. I can't so much as write for a dispatch box
for her (thinking an official of her scale must want one for her papers)
without its coming back full of pretty little match boxes as an offering, and
wrapped in a large contribution of old sheets.… I must give you the cream
of this last three or four days' letters. Firstly, Mr. Hookham, the bookseller,
sending down a parcel, says he “trusts to hear of the return of Miss N., as
he does not think, though convalescent, she can get well on the shores of
Bosphorus or Black Sea; that a General or Admiral can be replaced, but
there can be no successor to Miss N., her skill, her fortitude, her courage
cannot be replaced. I speak of courage in the most exalted sense that it is
possible to characterise the bravery and devotion of woman.” Then comes
a letter from a shipowner in the north of Scotland going to launch a
vessel, and wanting to call it after her, sends to have her name quite
“correct.” Next, Lady Dunsany saying that “Joan of Arc was not more a
creation of the moment and for the moment than F. Joan's was the same
unearthly influence carrying all before its spirit might—Joan's was the
same strange and sexless identity, which, belonging as it were neither to
man nor woman, seemed to disembody and combine the choicest results
of both, and then to sweep down conventionalities, prejudices, and
pruderies, with the clear, cold, crystal sceptre of its majestic purity. Joan's
mission, too, was the condensation of her country's moral and intellectual
power in the person of a young and single woman when the men of that
country were so many of them imbecile and effete! I think my parallel
runs pretty close.” Lord Dunsany adds that he has no time to write, so he
says, “ditto to Mrs. Burke,” and that I know he is “fanatico for Joan of Arc
rediviva, God bless her.” Then a bit from Lady Byron, saying, “even her
illness will advance her work as all things must for those who do all with
His aid,” and more that is most beautiful. Then 2 copies of the History of
 Women, with portrait of Miss N. to be sent to her “from the author,” and a
flaming extract from a County paper in a pamphlet, Stroll to Lea Hurst, 20
copies ditto, ditto, and a majestic effusion from the family grocer about
“heroic conduct,” “brave and noble Miss N.,” “identified with Crimean
success and sad disasters,” “posterity,” “arm of civilisation,” “rampant
barbarism,” &c. &c., and so on.

(To Florence Nightingale.) Dec. 8 [1855]. It has been curious[266] (as

your representative) how our Burlington Street room has seen Manning
and Maurice, Mr. Best and the Chancellor, Lady Amelia Jebb and
Mrs. Herbert, Lady Byron and Lady Canning, the extremes of all kinds
crowding in to help you in every way that they could devise. Then come in
tradespeople, all so intent on you; and working folk, your stoutest
supporters, and those you will care most for. And we are tenderly treated
and affectionately welcomed by one and all of all classes and opinions for
your sake, my dear, and very sweet to me is kindliness for your dear sake;
it seems as if it were part of you coming to meet me.

II

But Miss Nightingale's popularity was not limited to such circles as

those in which her family moved. Letters from soldiers in the Crimea
had made her known in thousands of humble homes, and she
became the heroine of the cottage, the workshop, and the alleys.
Old soldiers dropped into poetry about her, and rhymed broadsheets,
with rough woodcuts of the Lady with the Lamp, issued from
printers in Seven Dials and Soho. One of these songs, entitled “The
Nightingale in the East,” and intended to go to the tune of “The
Cottage and Water Mill,” was especially popular with its refrain:—

So forward, my lads, may your hearts never

fail,
You are cheer'd by the presence of a sweet
Nightingale.[181]
 Then from the same class of printing-offices there issued “Price
One Penny, The Only and Unabridged Edition of the Life of Miss
Nightingale, Detailing her Christian Heroic Deeds in the Land of
Tumult and Death, which has made her name most deservedly
Immortal, not only in England, but in all Civilized Parts of the World,
winning the Prayers of the Soldier, the Widow, and the Orphan.” The
poets and biographers were not only in Seven Dials. The Poet's
Corner of every newspaper, from Punch and the Spectator to the
smallest country journal, was devoted to the praise of the heroine.
Ingenious triflers were at work, and it was found that her anagram
was indeed, as an old definition has it, poesie transferred, and
Florence Nightingale became “Flit on, cheering angel.” Prize poems
at the universities pictured her, in the manner of such compositions,
walking fearlessly

Where strong men tremble and where brave hearts fail.

Then the musicians took up the Popular Heroine, and both now,
and after her return from the Crimea, sentimental songs, set to
music, were inscribed to her: “Angels with Sweet Approving Smiles,”
“The Shadow on the Pillow,” “The Soldier's Widow,” “The Woman's
Smile,” “The Soldier's Cheer”—this latter “played by the band of the
97th Regiment,”—“Die Soldaten Lebewohl,” “The Star of the East,”
and so forth. The stationers followed in the wake of the printers, and
brought out note-paper with a picture of Florence Nightingale as the
water-mark, or with lithographed views of “Lea Hurst, her home.”
Portraits of her were eagerly sought; and as the family were
unwilling to supply them, likenesses had to be invented to adorn
sentimental prints. Life-boats and emigrant-ships were christened
The Florence Nightingale. Children, streets, valses, and race-horses
were named after her. “The Forest Plate Handicap was won by Miss
Nightingale, beating Barbarity and nine others.” Tradesmen printed
portraits and short lives of her on their paper bags. At Fairs there
were “Grand Exhibitions of Miss Florence Nightingale administering
to the Sick and Wounded.” China figures, with no recognizable
likeness to her, but inscribed “Florence Nightingale,” were put on
sale. The public would not be denied. “Yes, indeed,” wrote Lady
Verney to her sister, “the people love you with a sort of passionate
tenderness that goes to my heart.”

Miss Nightingale did not relish all this. They had sent her various
supplies for the sick, and also a packet of “Lives,” “Portraits,” and the
like to Scutari. “My effigies and praises,” she wrote in reply, “were
less welcome. I do not affect indifference to real sympathy, but I
have felt painfully, the more painfully since I have had time to hear
of it, the éclat which has been given to this adventure. The small still
beginning, the simple hardship, the silent and gradual struggle
upwards, these are the climate in which an enterprise really thrives
and grows. Time has not altered our Saviour's lesson on that point,
which has been learnt successively by all reformers from their own
experience. The vanity and frivolity which the éclat thrown upon this
affair has called forth has done us unmitigated harm, and has
brought mischief on (perhaps) one of the most promising enterprises
that ever set sail from England. Our own old party which began its
work in hardship, toil, struggle, and obscurity has done better than
any other.”

III

When it became known in England that Miss Nightingale had

recovered from her illness, and had resolved to remain at her post
until the end of the war, a movement at once sprang up for marking
in some public manner the nation's appreciation of her services and
her devotion. There was at first some idea, as Lady Verney wrote, of
a personal testimonial in the “teapot and bracelet” kind. Mrs.
Herbert, who was consulted in the matter, knew her friend well
enough to be certain that Miss Nightingale would decline to accept
any such proposal. The only form of testimonial to which she would
ever listen was something to enable her the better to carry on her
work for others. Miss Nightingale was written to, and replied, in
accordance with Mrs. Herbert's expectation, that she must absolutely
decline any testimonial of a personal character. Her friends knew
well that what she would best like was the establishment in one
form or another of “an English Kaiserswerth.” This suggestion was
accordingly put before her, and she was asked to submit a plan. Her
reply was, again, very characteristic. Immersed in the crowded work
of the moment, she was in no mood to make future plans; but she
took the earliest opportunity of intimating that, whatever the plan
might be, she must be the autocrat of it. “Dr. Bence-Jones has
written to me,” she said (Sept. 27), “for a plan. People seem to think
that I have nothing to do but to sit here and form plans. If the public
choose to recognize my services and my judgment in this manner,
they must leave those services and that judgment unfettered.” She
was experiencing enough of fetters in the East to last her for a
lifetime. An influential Committee was formed, on which Mr. Sidney
Herbert and Mr. S. C. Hall served as honorary secretaries, and it was
decided to raise a fund for the establishment of some School for
Nurses, under a Council, to be nominated by Miss Nightingale. A
public meeting was called for November 29, 1855, at Willis's Rooms,
“to give expression to a general feeling that the services of Miss
Nightingale in the hospitals of the East demand the grateful
recognition of the British people.” The room proved far too small. It
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