Book Description

Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases pulls together all of the vital information about the most commonly used databases, analytical tools, and tables used in sequence analysis.The book is partitioned into three fundamental areas to help you maximize your use of the content. The first section, "Databases" contains examples of flatfiles from key databases (GenBank, EMBL, SWISS-PROT), the definitions of the codes or fields used in each database, and the sequence feature types/terms and qualifiers for the nucleotide and protein databases.The second section, "Tools" provides the command line syntax for popular applications such as ReadSeq, MEME/MAST, BLAST, ClustalW, and the EMBOSS suite of analytical tools. The third section, "Appendixes" concentrates on information essential to understanding the individual components that make up a biological sequence. The tables in this section include nucleotide and protein codes, genetic codes, as well as other relevant information.Written in O'Reilly's enormously popular, straightforward "Nutshell" format, this book draws together essential information for bioinformaticians in industry and academia, as well as for students.If sequence analysis is part of your daily life, you'll want this easy-to-use book on your desk. ... Read more

Reviews (3)

Sequence Analysis: Not in a Nutshell
The O'Reilly Press is normally the gold standard when it comes to very well-written and very well-edited hard science documents. That is why I purchased this one. Sadly, this falls very far below the norm. The first 73 pages of the text may be skipped. Most of the rest is EMBOSS. Sadly, you can get this directly, and freely, from the original authors. Just use a normal search and type "EMBOSS". Nothing else pertains.

Wayne

from a bioinformatics student and programmer
I picked this book up at BioCon 2003 and, to be honest, I wasn't sure at first how useful it was going to be. Flipping through a few of the sections, it seemed to be little more than an assemblage of man pages for each of the tools and programs it covered. So I put it on a shelf above my monitor at work for a while and as the days went by I found myself grabbing it more and more often to look something up.

For example, I found myself needing reminding of the option for tabular output when doing a psi-blast. Grab the book ... a ha! ... -m 8. You can use the man pages or tutorials for many of things like this but sometimes there is a lot to wade through to find what you were looking for. Also, if you're like me you like the feel of a book sometimes and the ability to scrawl notes in the margins. It's just nice having all the options right there on the page.

To be fair to the authors, I don't think that Chia-hsiu Tu was very accurate in his review by saying that "this books focus on EMBOSS only" (sic). EMBOSS coverage does make up about 58% of the book, but it is a suite of 150 useful programs. Unless you want only a sentence or two about each one you're going to have to use up a few pages. You get just enough info to learn about each and a quick guide to their usage. If you want to know more, there are links to their full documentation online.

Some sections are stronger than others. The MEME/MAST chapter, for instance, doesn't just list out options but has great command line examples and a paragraph for each explaining what is going on. On the other hand, I wanted to use stretcher (in the EMBOSS package) and there was only a quick example (the syntax of which didn't work for me) and a listing of six options. I needed to find out how to make it work in a non-interactive way and write its output to STDOUT, neither of which were illustrated (-auto and -stdout, by the way).

Ok, let's get to what this book covers. The first section goes really in depth to cover the data-exchange formats that we nerds find ourselves writing parsing scripts for all the time. (yes, yes, bioperl, biojava, etc. are great, but they aren't in this book. Hopefully one will cover them soon.) What I found most useful were the example files for each format (EMBL, DDBJ, Genbank, FASTA, SWISS-PROT, PFAM, & PROSITE) and the tables that were laid out for them. For example, there are nice little tables listing every feature (62 at my count) and feature qualifier (74!) that you can expect to find in a DDBJ/EMBL/Genbank file. And for each of those there is a little descripton of what they represent. Very nice.

The second part of the book covers these specific tools: ReadSeq, the BLAST suite (7 progs), BLAT, CLUSTALW, HMMER (10 progs), MEME, MAST, and the EMBOSS suite (~150 progs). These sections are pretty decent and while you won't find much info on how the algorithms behind the programs work, you will have everything you need to run the programs and fine-tune their options to control their behavior.

Lastly, the third part of the book has a really valuable quick reference of a variety of things such as a listing of the amino acids, their 1 and 3-letter abbreviations, structures and properties. In the genetic codes section you'll be able to quickly remind yourself that the transcriptional product for AUA in invertebrate mitochondriates differs from the norm, coding for methionine instead of isoleucine. (you knew that right?)

On the whole, I think this reference is a great review of the most common tools out there for sequence analysis and a quick guide to their use. While at times examples and verbose explanations are lacking, one must keep in mind that this is a book in the "nutshell" series, not in the "definitive guide" one. If you find yourself scouring for online docs and searching man pages for special options often, you should definitely get this book.

an excellent rteference book
This books focus on EMBOSS only, a high quality open source bioinformatic toolkit. It can be a useful reference book when write web interface of those programs in this book. Also it provides the urls where we can download from? where the original idea come from? ... Read more

Book Description

Gene Silencing by RNA Interference: Technology and Application provides background in the field and describes methods and protocols for gene silencing. It offers a general introduction to the subject of gene silencing and RNA interference and focuses on technical details of the various methods of producing siRNAs and other RNAi tools. The final chapters of the book detail the application of RNAi to dissect gene function in a number of biological systems, including cell-free systems, cultured cells, and whole organisms. This book is a comprehensive guide to gene silencing by RNA interference methods for beginners and experienced professionals in the field. ... Read more

Book Description

Introduction to Bioinformatics by Arthur Lesk is a timely and much-needed textbook which provides an accessible and thorough introduction to a subject which is becoming a fundamental part of biological science today. As a pioneer of the use of bioinformatics techniques in research, Dr Lesk brings unrivalled experience and expertise to the study of this field. The aim of the book is to generate an understanding of the biological background of bioinformatics, and to integrate this with an introduction to the use of computational skills. Without describing computer science or sophisticated programming skills in detail, the book supports and encourages the application of the many powerful computational tools of bioinformatics in a way that is both relevant to and stimulating for the reader. The book contains numerous problems and innovative Weblems (for Web-based Problems) to encourage students to engage with the subject and with the accompanying web site and to develop a working understanding and appreciation of the power of bioinformatics as a research tool. ... Read more

Book Description

From the nano-world of rusty proteins and magnetic compasses in bacteria to the macroscopic structures of oyster shells, corals, ivory, bone and enamel, biology has evolved a new type of chemistry that brings together the synthesis and construction of hard and soft matter for the design of functionalized inorganic-organic materials. The process that gives rise to these small and large inorganic-based structures of life is called biomineralization. This book looks at the chemical principles and concepts of biomineralization and their application in the new field of biomimetic materials chemistry. ... Read more

Reviews (1)

Great Book !
This a great book that covers the growing area of biomineralization. The concepts and the processes of biomineralization are well explained. I would recommend this book to anyone interested in learning more about biomineralization. ... Read more

Reviews (1)

From IJSM Vol 15, No 4 December 2001
This new millennium belongs to biotechnology. Rapid progress is being made in minerals processing based on biological principles. Microorganisms can play a beneficial role in all facets of minerals processing, from mining to waste disposal and management. Biohydrometallurgical extraction of metals from a wide variety of ores is being commercially practiced all over the world and especially in Canada, the United States, Russia, South America, Australia, and Europe. The interactions among biotechnology, metals, and minerals are relevant to a number of emerging in interdisciplinary areas such as biogenesis and biomineralization, biomaterials processing and biomimetics, ceramics and biomedical engineering, biomineral beneficiation, bioleaching, biocorrosion, biofouling, biodeterioration, and bioenvironmental control. This book contains 18 articles divvied into four main sections titled Biobeneficiation; Bioleaching; Bioremediation; and Biominerilaztion. Written by industry experts, the book provides the technical knowledge necessary to complete in this arena by presenting specific detailed technologies and real-world case studies. ... Read more

Book Description

This state-of-the-art reference integrates the latest knowledge on microfiltration and ultrafiltration membrane chemistry, and characterization methods with the engineering and economic aspects of device performance, device and module design, process, and applications. ... Read more

Book Description

In the face of rapid advances in medical research and treatment, bioethics has become a serious social concern. Originally published in 1996 and later chosen by World magazine as one of the top 100 books of the twentieth century, Gilbert Meilaender’s "Bioethics" covers a wide range of pressing bioethical issues and offers discerning guidance on how Christians ought to think about them.

In admirably clear language Meilaender discusses abortion, assisted reproduction, genetic advance and prenatal screening, care for the dying and euthanasia, human experimentation, and more. This new edition of his Bioethics features updated information throughout, a fuller discussion of human embryos — including stem cell research — and a thorough rewrite of the chapter on organ donation. ... Read more

Reviews (3)

Bioethics: A Primer for Christians
In recent times, with the advances in human reproductive technologies, cloning, organ transplants, contraceptive technologies, and abortifacients, it is necessary to provide clear moral answers to these ethical questions that face medical science today. The author's book provides an ethic based on Christian principles. The author does this by looking at life as a gift from God.

The first chapter of the book describes the basic elements in the Christian vision of the world. Christians in baptism are called to be members of the body of Christ. They are called to form a bond with each other; they are called into a community. Christians are created in freedom for communion with God. This freedom has its limits.

In chapters two through four, he argues that parenthood does not mean a right to have a child. The child is begotten and not made. Parents must not seek to have a child at all cost, not even in adoption. On abortion, the author argues that the life of the child in the womb is God's creation and is part of the world God came to redeem.

Chapters five and six discuss genetic advances and pre-natal screening. Gene type therapy makes children that come after us the products that we have molded. Pre-natal screening tends to separate the natural connection between mother and child and making parental commitment to offspring tentative and conditional.

In chapters six through eight, the author says suicide and euthanasia are attempts at being creators rather than creatures. Creatures do not have the ultimate judgment about a person. Christians have the responsibility of standing with the suffering to give them care and not minimize suffering. However, refusing a useless and excessively burdensome treatment is not immoral. Patients need to know the truth and to participate inthe decision making process. Living wills and health care power of the attorney are helpful where the patient is incapable of making a decision.

Chapters nine and ten discuss two gifts of the body, organ donation and human experimentation. Every gift of the body can be well given if a person understands him or herself as a gift rather than creators. People must freely and voluntarily give their consent in order to participate in medical research.

In the last chapter, the author discusses sickness and health. God is present in our illnesses and Christians must continue to live in this hope. Physicians ought not to see themselves as saviors but must cooperate with powers beyond theirs.

The author made logical and consistent arguments throughout the book. He supports his thesis with authoritative facts drawn from social events, medical advance and reputable authors. His style of writing is simple and devoid of words that will confuse the average reader. The major weakness with the book is the failure to give a more pastoral twist. The treatment of life's starting point is vague.

I highly recommend this book to anyone who desires knowing more about biomedical ethics and especially to all students of the medical sciences.

Bekeh Utietiang
School of Theology/Religious Studies
The Catholic University of America
Washington, DC.

Delivers what it promises: primer on bioethics
No pretenses about this book, upfront and straightforward that this is a primer on bioethics from a conservative Christian perspective.

He does a great job meeting his promises, providing intros to the topics of assisted reproduction, abortion, gene therapy, genetic research, prenatal screeening, suicide and euthanasia, organ donation, and research sensitive issues to humans.

He is unapologetic for not providing a survey of Christian opinions nor for trying to be faithful to his understanding (Lutheran) of Biblical truths.

He is sensitive in providing not a minimalistic, common denominator, public policy view, but one that is sensitive to the pro-life, Creator God who sustains all and will judge us at the end.

Possibly the only improvement I can see is the lack of a recommended reading list for those interested in pursuing topics further without reading journals, etc.

This book shall bless the church both in indiviudal Christians reading it and also for Bible study groups.

Review
This book is an overview, from a Christian perspective, of some of the current issues in clinical ethics or bioethics.While Dr Meilanader's viewpoint may differ significantly from that of many evangelical Christians or Catholics, his application of Christian principles to bioethical questions is very well done.I would strongly recommend this book to those interested in beginning to learn about issues in bioethics with a particular emphasis on the Christian perspective.For those interested in a deeper look at the issues, this book would serve only as an introduction. ... Read more

Book Description

Offers current data on delivery systems and therapeutic strategies, gene expression and detection, and disease targets and therapeutic strategies. Presents results and prospects in gene therapy clinical trials, other cell-based therapies and trials, and regulatory issues. Topics include optimization of non-viral gene therapeutics, gene therapy for cancer, and DNA vaccines. ... Read more

Book Description

Optical Biosensors provides the most comprehensive analysis of optical biosensors and relevant technologies to date. It focuses both on current state of the art technologies and new advances that will influence the future of optical biosensor development, including several technological advances not yet greatly explored within this field.

The book is divided into two parts: The first part focuses on present technology and here leaders in each field describe the underlying principles behind each technology. The authors then enumerate the types of applications for which it has been tested, provide opinions about the advantages and disadvantages of the biosensor and philosophize on future developments using that particular biosensor.

The second part deals with the science for future technology developments including four different methods for producing new recognition elements (genetic engineering of proteins, chemical synthesis, ... Read more

Book Description

Protein Biotechnology and Biochemistry is a complete and definitive source of information for all those interested in the area, providing a broad overview of the various medical, diagnostic and industrial uses of proteins. It covers basic biochemical principles as well as providing a comprehensive survey of products currently available or under development.

• The new edition has been thoroughly updated with new material.
• The key difference is that this new edition will include more "pure" biochemistry.
• There are two completely new chapters: Protein Structure - an overview and Novel Proteins from Novel Sources.

... Read more

Book Description

Today's resources on bloodstain analysis are still based on methods that were derived in the 1920s.Although medical and clinical research have provided a growing body of information on blood composition and behavior, this information has been ignored in favor of historical bloodstain analysis methods-until now.With 25 years of experience in the field, author Anita Wonder shows how to use these new methods for interpreting bloodstains, including non-Newtonian fluid behavior (a process that does not conform to Sir Isaac Newton's laws of motion) and three-dimensional dispersion modeling.

Blood Dynamics focuses on how to accurately identify eight bloodstain pattern types and their permutations. It covers every aspect of bloodstain analysis, and shows how some standard practices of reconstruction are not only unnecessary for identification of blood dynamics, but can even be misleading.

This book presents completely new scientific evaluations of blood dynamics and will fundamentally change the way in which bloodstains are interpreted.As such, it will be required reading for anyone who deals with blood evidence at the crime scene, in the lab, or in the courtroom.

*Presents groundbreaking new methods for interpreting bloodstains, including non-Newtonian fluid behaviour and three-dimensional dispersion modelling
*Covers every aspect of bloodstain analysis
*Focuses on how to accurately identify eight bloodstain pattern types and their permutations
*Author, Anita Wonder has 25 years of experience in the field of blood dynamics ... Read more

Reviews (2)

Excellent overview of the subject matter and well written!
The text provides an excellent overview of biotechnology for a person at the College level. The book is probably too shallow in depth for someone who wants to actually major in the subject matter. Nonetheless, the book serves its intended purpuse well to introduce biotechnology at a reaonably sophisticated level to the student. The book starts with the basics of organic chemistry principles and expands them to biochemistry. Well done!
All the important technological and commercial concepts relevant to biotechnology are present and explaned well through text as well as diagrams. Perhaps one aspect that science books don't emphasize is writting style. The books is extremely clear and well written and can probably serve as an example of good technical writting style. I highly recommend the book to anyone who is serious about wanting to understand Biotechnology. As long as you hand Freshmand chemistry this book should serve you.

Just the basics
If you are looking for a clear and interesting summary of many key concepts of Biotechnology, this book is for you. The author does a nice job of distilling the important concepts for both the scientist and layman alike. For the scientist, the book provides a nice review of the basics, and for the layman, it explains many difficult principles. At the end of each chapter the author also provides a lively discussion of some interesting practical applications and problems solved by Biotechnology. ... Read more

Book Description

A valuable resource for researchers and workers in the fields of both pharmaceuticals and biotechnology as well as undergraduates in biochemistry, applied biology, biomedical sciences and pharmacy, this book compares established techniques of antibody production with the new. Antibody structure and the implications of antibody engineering are fully discussed, and a case study approach illustrates how antibodies are finding increasing use in the diagnosis and treatment of disease. The volume ends with commercial expression, purification and large-scale manufacture of antibodies and their future potential, particularly as therapeutic agents. ... Read more

Book Description

Recent advances in medical research have shown that embryonic stem cells can be used to treat some of the most debilitating diseases, notably Parkinson's disease, spinal injuries, and nerve cell damage.Yet the troubling ethical downside of this promising technology is that up till now the main source of stem cells has been tissue taken from aborted fetuses.This practice has raised sharp criticisms from opponents of abortion who charge that science is capitalizing on an abhorrent procedure.Proponents of stem cell research argue that scientists are making legitimate use of already aborted fetuses and it is unfair to deprive those suffering from serious diseases and injuries of a potentially revolutionary therapy.The issue became so divisive that in August 2001, President Bush addressed the nation on new developments in stem cell research and the ethical dilemmas this technology poses.Should such research be permitted?What, if any, moral, religious or political objections might be raised?

Philosophers Michael Ruse and Christopher A. Pynes have compiled this valuable collection of articles by noted experts to address all aspects of this question by examining one of today's most challenging and fiercely debated new areas of science.They explain the scientific research, explore the medical promise that it offers, and present the many sides of the ethical, religious, and policy debate.The contributors--scientists, medical practitioners, philosophers, theologicans, historians, and policy analysts--offer a variety of perspectives, to give readers the critical tools they need to shape an informed position on the topic.This important resource will be useful and accessible to educated readers with no prior knowledge of this contentious issue. ... Read more

Book Description

"If ever there was need and opportunity for Christians to shape culture, it is now," write Charles W. Colson and Nigel M. de S. Cameron.

The contributors to "Human Dignity in the Biotech Century" make the case that biotechnology is the next front in the battles over ethics and public policy, and Christians need to bring their influence to bear on the debates. These twelve essays, contributed by scholars and leaders who are part of Colson’s Wilberforce Forum, alert readers to the ethical and legal challenges we face in the new genetics, involving embryo research, stem cell research, cloning, genetic engineering, gene therapy, pharmacogenomics, cybernetics, nanotechnology and abortion.

"We need to get a grip on biotechnology and the bioethical considerations that go along with it," Colson challenges. "It is time for people to get educated, to think about these profound moral questions that affect the future of the human race." ... Read more

Book Description

European law has been faced with increasingly complex issues emerging from rapid developments in pharmaceutical medicine and biotechnology. A team of distinguished European legal practitioners and academics reassess the impact of European law on health care and pharmaceutical law. The essays are grouped under four themes: free movement of goods and persons, competition and intellectual property; European drug regulation; biotechnology; and product liability and transnational health care litigation. This important study offers a valuable resource for the pharmaceutical and biotechnology industries, as well as legal academics and practitioners. ... Read more

Book Description

Book Description

"Biotechnology" as generally understood is a misnomer, having less to do with biology than with generating profits from genetic manipulation. The corporatizing of genetic science is just the latest risky manifestation of a dysfunctional industrial paradigm based on consuming natural capital and producing toxic waste-an economic model totally at odds with the evolutionary intelligence of living systems.But there is another way. The "true biotechnologies," described in this second volume in the Bioneers series, are working strategies grounded in the innate complexity, relatedness, and sustainability of natural ecosystems. The contributors to this volume are visionary leaders in fields such as biomimicry (mimicking nature in order to restore nature and serve human ends harmlessly), "living machines" that break down toxics biologically, natural design for industrial processes and buildings, and the restoration of natural capital. Their guiding principles include diversity, kinship, symbiosis, reciprocity, and community. These brilliant innovators illuminate a future environment of hope by "wedding human ingenuity with the wisdom of the wild," as contributor John Todd puts it.Human beings are a keystone species with an essential role to play in the ecological well-being of our world; we are only just learning how to go about it. Sector by sector-from energy and agriculture to transportation, industrial production, and land management-the true biotechnologies described here show how nature has already orchestrated a symphony of intelligent design that we can emulate and adapt, to the benefit of humanity and all life on Earth. ... Read more