Here are 11 books that Programming Perl fans have personally recommended if you like
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Mathematics and chemistry were my strongest subjects at school, and I started programming computers when I was 16, but life seemed most important. Hence I studied biochemistry in university but moved into molecular biology with programming to assist the data analysis. My track record in successfully predicting new biology through computing led to a pharmaceutical company recruiting me to do bioinformatics for them. However, not content with studying genes and proteins, I pushed for bioinformatics to move up into metabolism, anatomy, and physiology. That’s when I discovered systems biology. My international reputation lies at this interface and includes discoveries in microbial physiology, botany, agriculture, animal biology, and antenatal diseases.
This book vindicates my long-held view that biological objects do not act in isolation but interact with other things to make a living whole. It confirms my opinion that genes are not the master controllers of living things.
Furthermore, it showed me that systems occur at different physical scales (molecules, cells, organs, organisms, populations), that the systems at these scales influence each other, and that no scale is dominant. To understand biological/medical phenomena, including human consciousness, one must look at the (multi-scale) systems, not their individual components, in isolation.
Finally, I found it a lot of fun to read because it uses hypothetical stories to illustrate points. For example, silicon-based aliens visit Earth but fail to understand why certain things and people behave the way that they do.
What is Life? Decades of research have resulted in the full mapping of the human genome - three billion pairs of code whose functions are only now being understood. The gene's eye view of life, advocated by evolutionary biology, sees living bodies as mere vehicles for the replication of the genetic codes.
But for a physiologist, working with the living organism, the view is a very different one. Denis Noble is a world renowned physiologist, and sets out an alternative view to the question - one that becomes deeply significant in terms of the living, breathing organism. The genome is…
Mathematics and chemistry were my strongest subjects at school, and I started programming computers when I was 16, but life seemed most important. Hence I studied biochemistry in university but moved into molecular biology with programming to assist the data analysis. My track record in successfully predicting new biology through computing led to a pharmaceutical company recruiting me to do bioinformatics for them. However, not content with studying genes and proteins, I pushed for bioinformatics to move up into metabolism, anatomy, and physiology. That’s when I discovered systems biology. My international reputation lies at this interface and includes discoveries in microbial physiology, botany, agriculture, animal biology, and antenatal diseases.
Of the various books available on this subject, I very much prefer this one because it makes it far easier to do systems biology.
First, it shows you how to view biological regulatory processes as a set of interacting components and their effect on each other. This alone can give clues to the behaviour of the system under different circumstances. However, it then goes on to show how these processes can be defined mathematically, which then enables us to get a quantitative view of what is going on.
When the predicted and observed numbers don’t match, we know that there is a gap in our knowledge and, hence, the place to discover new biology. Using this approach, I have.
... superb, beautifully written and organized work that takes an engineering approach to systems biology. Alon provides nicely written appendices to explain the basic mathematical and biological concepts clearly and succinctly without interfering with the main text. He starts with a mathematical description of transcriptional activation and then describes some basic transcription-network motifs (patterns) that can be combined to form larger networks. - Nature
[This text deserves] serious attention from any quantitative scientist who hopes to learn about modern biology ... It assumes no prior knowledge of or even interest in biology ... One final…
Mathematics and chemistry were my strongest subjects at school, and I started programming computers when I was 16, but life seemed most important. Hence I studied biochemistry in university but moved into molecular biology with programming to assist the data analysis. My track record in successfully predicting new biology through computing led to a pharmaceutical company recruiting me to do bioinformatics for them. However, not content with studying genes and proteins, I pushed for bioinformatics to move up into metabolism, anatomy, and physiology. That’s when I discovered systems biology. My international reputation lies at this interface and includes discoveries in microbial physiology, botany, agriculture, animal biology, and antenatal diseases.
This book turns on its head what I was taught about what controls metabolite flow through a pathway. It covers highly remarkable discoveries concerning which steps control changes in metabolite levels: those at the end rather than the start of pathways. This is amazing because it explains why decades of effort by bioengineers to overproduce particular metabolites was unsuccessful.
In response to a request from such a project, I explained how to block the inhibitory regulation by the early pathway step but added that, according to metabolic control theory, this would leave the end-product levels unchanged. I was correct on both counts! When my group later provided results from using a systems biology approach, they achieved their production target levels.
Mathematics and chemistry were my strongest subjects at school, and I started programming computers when I was 16, but life seemed most important. Hence I studied biochemistry in university but moved into molecular biology with programming to assist the data analysis. My track record in successfully predicting new biology through computing led to a pharmaceutical company recruiting me to do bioinformatics for them. However, not content with studying genes and proteins, I pushed for bioinformatics to move up into metabolism, anatomy, and physiology. That’s when I discovered systems biology. My international reputation lies at this interface and includes discoveries in microbial physiology, botany, agriculture, animal biology, and antenatal diseases.
This is one of my most valued reference books, and I have referred to it many times.
With some explanatory text, it consists of a set of maps of biochemical pathways, differentiating between organism kingdoms, and includes how specific metabolites regulate the activity of particular enzymes. The pathways are very easy to find and easy to interpret. In contrast, the online equivalents can be difficult to interpret for a variety of reasons.
The book has the added advantage that it does not need a power supply or an internet connection and can be used in a far wider range of temperatures than computer hardware.
The pathways and networks underlying biological function
Now in its second edition, Biochemical Pathways continues to garner praise from students, instructors, and researchers for its clear, full-color illustrations of the pathways and networks that determine biological function.
Biochemical Pathways examines the biochemistry of bacteria, plants, and animals. It offers a quick overview of the metabolic sequences in biochemical pathways, the chemistry and enzymology of conversions, the regulation of turnover, the expression of genes, the immunological interactions, and the metabolic background of health disorders. A standard set of conventions is used in all illustrations, enabling readers to easily gather information and…
Since I was a kid, I’ve been passionate about technology and had a clear vocation to work with computers. I’ve been a developer for more than 20 years now, spending half of them mainly in the Python environment, and I’ve always been interested in improving my skills. While it’s true that software development is a field that changes constantly and technology evolves at great speed, there are some elements that remain relatively unchanged and can be used to compound knowledge and ability. In particular, the elements that are closer to the human element, teamwork, coordination, etc. are quite stable over time.
A very personal recommendation, as it is about Vim, a very particular text editor that can be difficult to learn at first, but this is the best technical book that I’ve ever read. I use Vim as my main editor and this book makes an astonishing job in clearly explaining why it works the way it works. This book gets you into the proper mindset to use Vim, making it click internally and from there on, to feel way more natural and powerful. Even if you don’t want to use Vim as your main editor, it’s ubiquitous and it’s available by default on a huge amount of computers, making being comfortable with its usage a really powerful tool in a lot of situations.
Vim is a fast and efficient text editor that will make you a faster and more efficient developer. It's available on almost every OS--if you master the techniques in this book, you'll never need another text editor. Practical Vim shows you 120 vim recipes so you can quickly learn the editor's core functionality and tackle your trickiest editing and writing tasks. Vim, like its classic ancestor vi, is a serious tool for programmers, web developers, and sysadmins. No other text editor comes close to Vim for speed and efficiency; it runs on almost every system imaginable and supports most coding…
Like most geeks, I've always loved efficiency and productivity. Coming from a Windows-dominated world, the command line I was faced with in my CompSci degree was Initially mystifying, but over time I have come to see it as the most powerful human-computer interface out there. After spending years wresting with the command line at work, I decided to write a book on bash, and have blogged extensively on this and related topics. I also run live courses on bash and the command line for O'Reilly. There's nothing I enjoy more than opening people's eyes to the power of the shell!
Once I'd covered the command line basics, then I bought this book and kept it by my bed for a couple of years, imbibing its contents over and over.
It contains so many examples of how the command line can be used in real-world situations, as well as more practical advice and timeless tips. It feels like you've got four experts at your shoulder helping you get better.
It's so good I'm going to start re-reading it as soon as I've finished writing this.
With the growing popularity of Linux and the advent of Darwin, Unix has metamorphosed into something new and exciting. No longer perceived as a difficult operating system, more and more users are discovering the advantages of Unix for the first time. But whether you are a newcomer or a Unix power user, you'll find yourself thumbing through the goldmine of information in the new edition of Unix Power Tools to add to your store of knowledge. Want to try something new? Check this book first, and you're sure to find a tip or trick that will prevent you from learning…
Ever since I studied control theory as an undergrad chemical engineer, mathematical models of complex phenomena have fascinated me. Mathematical models have the uncanny ability to uncover key aspects of biological systems, whose complexity poses a great challenge for understanding. As a researcher in systems biology for over 15 years, I have enjoyed reading several books that explore the exciting interface between computation and biology, trying to capture the burgeoning literature on this rapidly advancing field. I hope you enjoy these books and will join these authors on an exciting journey into the cartography of molecular networks underlying every living cell, using a variety of mathematical models!
An outstanding and authoritative reference on metabolic networks. Discusses all the mathematical foundations of constraint-based methods, followed by detailed discussions of various constraint-based modelling methods. Despite the age, this remains a thorough and excellent account of constraint-based modelling. A revised second edition of this book presents a more detailed overview of metabolic networks in different organisms and is up-to-date with several advances in the field. Palsson is one of the leaders in the field of systems biology and metabolic networks, and his lab is home to many of the most important constraint-based modelling methods, such as flux balance analysis.
Recent technological advances have enabled comprehensive determination of the molecular composition of living cells. The chemical interactions between many of these molecules are known, giving rise to genome-scale reconstructed biochemical reaction networks underlying cellular functions. Mathematical descriptions of the totality of these chemical interactions lead to genome-scale models that allow the computation of physiological functions. Reflecting these recent developments, this textbook explains how such quantitative and computable genotype-phenotype relationships are built using a genome-wide basis of information about the gene portfolio of a target organism. It describes how biological knowledge is assembled to reconstruct biochemical reaction networks, the formulation of…
I've been a C# programmer for 23 years, and am passionate about the language. It is the perfect balance of power and ease of use, and each year it is extended by its amazing development team. I've used C# to build stand-alone applications, mobile applications, APIs, and database applications and I've never felt constrained. Finally, C# lends itself to best practices and design patterns, and continues to rise in popularity, especially with professional software developers.
This is the definitive reference book on C#. The Albahari brothers have been writing about C# since the early bits, and they know the language inside and out. While this is a hefty book, you will find yourself using it frequently, and you'll be impressed by its comprehensiveness and utility.
When you have questions about C# 10 or .NET 6, this best-selling guide has the answers you need. C# is a language of unusual flexibility and breadth, and with its continual growth, there's always so much more to learn. In the tradition of O'Reilly's Nutshell guides, this thoroughly updated edition is simply the best one-volume reference to the C# language available today.
Organized around concepts and use cases, this comprehensive and complete reference provides intermediate and advanced programmers with a concise map of C# and .NET that also plumbs significant depths.
Some programmers learn through online articles, videos, and blog posts. Not me. I need a throughline—a consistent, expert distillation of the material to take me from where I am to where I want to be. I am not good at patching together information from disparate sources. I need a great book. I have a PhD in computer science education, and I want to know what helps people learn. More importantly, I want to know how we can use such discoveries to write more effective books. The books I appreciate most are those that demonstrate not only mastery of the subject matter but also mastery of teaching.
Learning to program is hard. We need teachers who remember this, who are patient, who support the learning process, who not only know how to teach but also know how to learn from their teaching. Severance is all of these things. I like the breezy but precise writing, sections on debugging, glossaries and exercises in each chapter, and discussion of common learner errors. Bonus feature: regular expressions.
Python for Everybody is designed to introduce students to programming and software development through the lens of exploring data. You can think of the Python programming language as your tool to solve data problems that are beyond the capability of a spreadsheet.
Python is an easy to use and easy to learn programming language that is freely available on Macintosh, Windows, or Linux computers. So once you learn Python you can use it for the rest of your career without needing to purchase any software.
This book uses the Python 3 language. The earlier Python 2 version of this book…
Like most geeks, I've always loved efficiency and productivity. Coming from a Windows-dominated world, the command line I was faced with in my CompSci degree was Initially mystifying, but over time I have come to see it as the most powerful human-computer interface out there. After spending years wresting with the command line at work, I decided to write a book on bash, and have blogged extensively on this and related topics. I also run live courses on bash and the command line for O'Reilly. There's nothing I enjoy more than opening people's eyes to the power of the shell!
Regular expressions are the cornerstone of command line wizardry.
They are used in pretty much all command-line tools, and all programming languages.
If you read this book, you'll have a deep understanding of what's going on, and the knowledge to go from hand-waving and guessing your way through regular expression writing to the mastery the book promises.
Regular expressions are an extremely powerful tool for manipulating text and data. They are now standard features in a wide range of languages and popular tools, including Perl, Python, Ruby, Java, VB.NET and C# (and any language using the .NET Framework), PHP, and MySQL. If you don't use regular expressions yet, you will discover in this book a whole new world of mastery over your data. If you already use them, you'll appreciate this book's unprecedented detail and breadth of coverage. If you think you know all you need to know about regular expressions, this book is a stunning eye-opener.…
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