Bioinformatics Club~ A club to promote bioinformatics

How to write Research Papers

2012-02-21T22:56:00.001-08:00

Writing is easy. All you do is stare at a blank sheet of paper until drops of blood form on your forehead. --- Gene Fowler

A major goal of this course is the development of effective technical writing skills. To help you become an accomplished writer, you will prepare several research papers based upon the studies completed in lab. Our research papers are not typical "lab reports." In a teaching lab a lab report might be nothing more than answers to a set of questions. Such an assignment hardly represents the kind of writing you might be doing in your eventual career.

Written and oral communications skills are probably the most universal qualities sought by graduate and professional schools as well as by employers. You alone are responsible for developing such skills to a high level.

Resources for learning technical writing

Before you begin your first writing assignment, please consult all of the following resources, in order to gain the most benefit from the experience.

General form of a typical research article
Specific guidelines (if any) for the assignment – see the writeups on individual lab studies
McMillan, VE. "Writing Papers in the Biological Sciences, Third Ed." New York: Bedford/St. Martin's, 2001. ISBN 0-312-25857-7 (REQUIRED for Bios 211, 311, recommended for other science courses that include writing)

As you polish up your writing skills please make use of the following resources

Instructor feedback on previous assignments
Common errors in student research papers
Selected writing rules (somewhat less serious than the other resources)

For Biosciences majors the general guidelines apply to future course work, as can be seen by examining the guidelines for the advanced experimental sciences research paper (Bios 311). Instructions for authors from the Journal of Biological Chemistry editorial board may be helpful as well. Their statement of editorial policies and practices may give you an idea of how material makes its way into the scientific literature.

General form of a research paper

An objective of organizing a research paper is to allow people to read your work selectively. When I research a topic, I may be interested in just the methods, a specific result, the interpretation, or perhaps I just want to see a summary of the paper to determine if it is relevant to my study. To this end, many journals require the following sections, submitted in the order listed, each section to start on a new page. There are variations of course. Some journals call for a combined results and discussion, for example, or include materials and methods after the body of the paper. The well known journal Science does away with separate sections altogether, except for the abstract.

Your papers are to adhere to the form and style required for the Journal of Biological Chemistry, requirements that are shared by many journals in the life sciences.

General style

Specific editorial requirements for submission of a manuscript will always supercede instructions in these general guidelines.

To make a paper readable

Print or type using a 12 point standard font, such as Times, Geneva, Bookman, Helvetica, etc.
Text should be double spaced on 8 1/2" x 11" paper with 1 inch margins, single sided
Number pages consecutively
Start each new section on a new page
Adhere to recommended page limits

Mistakes to avoid

Placing a heading at the bottom of a page with the following text on the next page (insert a page break!)
Dividing a table or figure - confine each figure/table to a single page
Submitting a paper with pages out of order

In all sections of your paper

Use normal prose including articles ("a", "the," etc.)
Stay focused on the research topic of the paper
Use paragraphs to separate each important point (except for the abstract)
Indent the first line of each paragraph
Present your points in logical order
Use present tense to report well accepted facts - for example, 'the grass is green'
Use past tense to describe specific results - for example, 'When weed killer was applied, the grass was brown'
Avoid informal wording, don't address the reader directly, and don't use jargon, slang terms, or superlatives
Avoid use of superfluous pictures - include only those figures necessary to presenting results

Title Page

Select an informative title as illustrated in the examples in your writing portfolio example package. Include the name(s) and address(es) of all authors, and date submitted. "Biology lab #1" would not be an informative title, for example.

Abstract

The summary should be two hundred words or less. See the examples in the writing portfolio package.

General intent

An abstract is a concise single paragraph summary of completed work or work in progress. In a minute or less a reader can learn the rationale behind the study, general approach to the problem, pertinent results, and important conclusions or new questions.

Writing an abstract

Write your summary after the rest of the paper is completed. After all, how can you summarize something that is not yet written? Economy of words is important throughout any paper, but especially in an abstract. However, use complete sentences and do not sacrifice readability for brevity. You can keep it concise by wording sentences so that they serve more than one purpose. For example, "In order to learn the role of protein synthesis in early development of the sea urchin, newly fertilized embryos were pulse-labeled with tritiated leucine, to provide a time course of changes in synthetic rate, as measured by total counts per minute (cpm)." This sentence provides the overall question, methods, and type of analysis, all in one sentence. The writer can now go directly to summarizing the results.

Summarize the study, including the following elements in any abstract. Try to keep the first two items to no more than one sentence each.

Purpose of the study - hypothesis, overall question, objective
Model organism or system and brief description of the experiment
Results, including specific data - if the results are quantitative in nature, report quantitative data; results of any statistical analysis shoud be reported
Important conclusions or questions that follow from the experiment(s)

Style:

Single paragraph, and concise
As a summary of work done, it is always written in past tense
An abstract should stand on its own, and not refer to any other part of the paper such as a figure or table
Focus on summarizing results - limit background information to a sentence or two, if absolutely necessary
What you report in an abstract must be consistent with what you reported in the paper
Corrrect spelling, clarity of sentences and phrases, and proper reporting of quantities (proper units, significant figures) are just as important in an abstract as they are anywhere else

Introduction

Your introductions should not exceed two pages (double spaced, typed). See the examples in the writing portfolio package.

General intent

The purpose of an introduction is to aquaint the reader with the rationale behind the work, with the intention of defending it. It places your work in a theoretical context, and enables the reader to understand and appreciate your objectives.

Writing an introduction

The abstract is the only text in a research paper to be written without using paragraphs in order to separate major points. Approaches vary widely, however for our studies the following approach can produce an effective introduction.

Describe the importance (significance) of the study - why was this worth doing in the first place? Provide a broad context.
Defend the model - why did you use this particular organism or system? What are its advantages? You might comment on its suitability from a theoretical point of view as well as indicate practical reasons for using it.
Provide a rationale. State your specific hypothesis(es) or objective(s), and describe the reasoning that led you to select them.
Very briefy describe the experimental design and how it accomplished the stated objectives.

Style:

Use past tense except when referring to established facts. After all, the paper will be submitted after all of the work is completed.
Organize your ideas, making one major point with each paragraph. If you make the four points listed above, you will need a minimum of four paragraphs.
Present background information only as needed in order support a position. The reader does not want to read everything you know about a subject.
State the hypothesis/objective precisely - do not oversimplify.
As always, pay attention to spelling, clarity and appropriateness of sentences and phrases.

Materials and Methods

There is no specific page limit, but a key concept is to keep this section as concise as you possibly can. People will want to read this material selectively. The reader may only be interested in one formula or part of a procedure. Materials and methods may be reported under separate subheadings within this section or can be incorporated together.

General intent

This should be the easiest section to write, but many students misunderstand the purpose. The objective is to document all specialized materials and general procedures, so that another individual may use some or all of the methods in another study or judge the scientific merit of your work. It is not to be a step by step description of everything you did, nor is a methods section a set of instructions. In particular, it is not supposed to tell a story. By the way, your notebook should contain all of the information that you need for this section.

Writing a materials and methods section

Materials:

Describe materials separately only if the study is so complicated that it saves space this way.
Include specialized chemicals, biological materials, and any equipment or supplies that are not commonly found in laboratories.
Do not include commonly found supplies such as test tubes, pipet tips, beakers, etc., or standard lab equipment such as centrifuges, spectrophotometers, pipettors, etc.
If use of a specific type of equipment, a specific enzyme, or a culture from a particular supplier is critical to the success of the experiment, then it and the source should be singled out, otherwise no.
Materials may be reported in a separate paragraph or else they may be identified along with your procedures.
In biosciences we frequently work with solutions - refer to them by name and describe completely, including concentrations of all reagents, and pH of aqueous solutions, solvent if non-aqueous.

Methods:

See the examples in the writing portfolio package
Report the methodology (not details of each procedure that employed the same methodology)
Describe the mehodology completely, including such specifics as temperatures, incubation times, etc.
To be concise, present methods under headings devoted to specific procedures or groups of procedures
Generalize - report how procedures were done, not how they were specifically performed on a particular day. For example, report "samples were diluted to a final concentration of 2 mg/ml protein;" don't report that "135 microliters of sample one was diluted with 330 microliters of buffer to make the protein concentration 2 mg/ml." Always think about what would be relevant to an investigator at another institution, working on his/her own project.
If well documented procedures were used, report the procedure by name, perhaps with reference, and that's all. For example, the Bradford assay is well known. You need not report the procedure in full - just that you used a Bradford assay to estimate protein concentration, and identify what you used as a standard. The same is true for the SDS-PAGE method, and many other well known procedures in biology and biochemistry.

Style:

It is awkward or impossible to use active voice when documenting methods without using first person, which would focus the reader's attention on the investigator rather than the work. Therefore when writing up the methods most authors use third person passive voice.
Use normal prose in this and in every other section of the paper – avoid informal lists, and use complete sentences.

What to avoid

Materials and methods are not a set of instructions.
Omit all explanatory information and background - save it for the discussion.
Omit information that is irrelevant to a third party, such as what color ice bucket you used, or which individual logged in the data.

Results

The page length of this section is set by the amount and types of data to be reported. Continue to be concise, using figures and tables, if appropriate, to present results most effectively. See recommendations for content, below.

General intent

The purpose of a results section is to present and illustrate your findings. Make this section a completely objective report of the results, and save all interpretation for the discussion.

Writing a results section

IMPORTANT: You must clearly distinguish material that would normally be included in a research article from any raw data or other appendix material that would not be published. In fact, such material should not be submitted at all unless requested by the instructor.

Content

Summarize your findings in text and illustrate them, if appropriate, with figures and tables.
In text, describe each of your results, pointing the reader to observations that are most relevant.
Provide a context, such as by describing the question that was addressed by making a particular observation.
Describe results of control experiments and include observations that are not presented in a formal figure or table, if appropriate.
Analyze your data, then prepare the analyzed (converted) data in the form of a figure (graph), table, or in text form.

What to avoid

Do not discuss or interpret your results, report background information, or attempt to explain anything.
Never include raw data or intermediate calculations in a research paper.
Do not present the same data more than once.
Text should complement any figures or tables, not repeat the same information.
Please do not confuse figures with tables - there is a difference.

Style

As always, use past tense when you refer to your results, and put everything in a logical order.
In text, refer to each figure as "figure 1," "figure 2," etc. ; number your tables as well (see the reference text for details)
Place figures and tables, properly numbered, in order at the end of the report (clearly distinguish them from any other material such as raw data, standard curves, etc.)
If you prefer, you may place your figures and tables appropriately within the text of your results section.

Figures and tables

Either place figures and tables within the text of the result, or include them in the back of the report (following Literature Cited) - do one or the other
If you place figures and tables at the end of the report, make sure they are clearly distinguished from any attached appendix materials, such as raw data
Regardless of placement, each figure must be numbered consecutively and complete with caption (caption goes under the figure)
Regardless of placement, each table must be titled, numbered consecutively and complete with heading (title with description goes above the table)
Each figure and table must be sufficiently complete that it could stand on its own, separate from text

Discussion

Journal guidelines vary. Space is so valuable in the Journal of Biological Chemistry, that authors are asked to restrict discussions to four pages or less, double spaced, typed. That works out to one printed page. While you are learning to write effectively, the limit will be extended to five typed pages. If you practice economy of words, that should be plenty of space within which to say all that you need to say.

General intent

The objective here is to provide an interpretation of your results and support for all of your conclusions, using evidence from your experiment and generally accepted knowledge, if appropriate. The significance of findings should be clearly described.

Writing a discussion

Interpret your data in the discussion in appropriate depth. This means that when you explain a phenomenon you must describe mechanisms that may account for the observation. If your results differ from your expectations, explain why that may have happened. If your results agree, then describe the theory that the evidence supported. It is never appropriate to simply state that the data agreed with expectations, and let it drop at that.

Decide if each hypothesis is supported, rejected, or if you cannot make a decision with confidence. Do not simply dismiss a study or part of a study as "inconclusive."
Research papers are not accepted if the work is incomplete. Draw what conclusions you can based upon the results that you have, and treat the study as a finished work
You may suggest future directions, such as how the experiment might be modified to accomplish another objective.
Explain all of your observations as much as possible, focusing on mechanisms.
Decide if the experimental design adequately addressed the hypothesis, and whether or not it was properly controlled.
Try to offer alternative explanations if reasonable alternatives exist.
One experiment will not answer an overall question, so keeping the big picture in mind, where do you go next? The best studies open up new avenues of research. What questions remain?
Recommendations for specific papers will provide additional suggestions.

Style:

When you refer to information, distinguish data generated by your own studies from published information or from information obtained from other students (verb tense is an important tool for accomplishing that purpose).
Refer to work done by specific individuals (including yourself) in past tense.
Refer to generally accepted facts and principles in present tense. For example, "Doofus, in a 1989 survey, found that anemia in basset hounds was correlated with advanced age. Anemia is a condition in which there is insufficient hemoglobin in the blood."

The biggest mistake that students make in discussions is to present a superficial interpretation that more or less re-states the results. It is necessary to suggest why results came out as they did, focusing on the mechanisms behind the observations.

Literature Cited

Please note that in the introductory laboratory course, you will not be required to properly document sources of all of your information. One reason is that your major source of information is this website, and websites are inappropriate as primary sources. Second, it is problematic to provide a hundred students with equal access to potential reference materials. You may nevertheless find outside sources, and you should cite any articles that the instructor provides or that you find for yourself.

List all literature cited in your paper, in alphabetical order, by first author. In a proper research paper, only primary literature is used (original research articles authored by the original investigators). Be cautious about using web sites as references - anyone can put just about anything on a web site, and you have no sure way of knowing if it is truth or fiction. If you are citing an on line journal, use the journal citation (name, volume, year, page numbers). Some of your papers may not require references, and if that is the case simply state that "no references were consulted."

Bioinformatics for Geneticists: A Bioinformatics Primer for the Analysis of Genetic Data

2012-02-14T03:51:00.000-08:00

By Michael R. Barnes

A fully revised version of the successful First Edition, this one-stop reference book enables all geneticists to improve the efficiency of their research.
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Biochemical Engineering and Biotechnology

2011-11-26T03:43:00.000-08:00

Extensive application of bioprocesses has generated an expansion in biotechnological knowledge, generated by theapplication of biochemical engineering to biotechnology. Microorganisms produce alcohols and acetone that are used in industrial processes. The knowledge related to industrial microbiology has been revolutionized by the ability of genetically engineered cells to make many new products. Genetic engineering and gene mounting has been developed to enhance industrial fermentation. Ultimately, these bioprocesses have become a new way of developing commercial products.

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Artificial Intelligence for Games, Second Edition

2011-08-22T05:02:00.000-07:00

Artificial Intelligence for Games, Second Edition by Ian Millington, John Funge
MK | 2009 | ISBN: 0123747317 | 896 pages | PDF | 15 MB

Creating robust artificial intelligence is one of the greatest challenges for game developers, yet the commercial success of a game is often dependent upon the quality of the AI. In this book, Ian Millington brings extensive professional experience to the problem of improving the quality of AI in games. He describes numerous examples from real games and explores the underlying ideas through detailed case studies. He goes further to introduce many techniques little used by developers today. The book's associated web site contains a library of C++ source code and demonstration programs, and a complete commercial source code library of AI algorithms and techniques.

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Artificial Intelligence A Systems Approach

2011-08-22T04:56:00.000-07:00

M. Tim Jones, "Artificial Intelligence: A Systems Approach " Chapman | 2007 | ISBN: 0977858235 | 500 pages | PDF | 6,5 MB

This book offers students and AI programmers a new perspective on the study of artificial intelligence concepts. The essential topics and theory of AI are presented, but it also includes practical information on data input & reduction as well as data output (i.e., algorithm usage). Because traditional AI concepts such as pattern recognition, numerical optimization and data mining are now simply types of algorithms, a different approach is needed. This sensor / algorithm / effecter approach grounds the algorithms with an environment, helps students and AI practitioners to better understand them, and subsequently, how to apply them. The book has numerous up to date applications in game programming, intelligent agents, neural networks, artificial immune systems, and more.

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DNA Fingerprinting in Plants: Principles, Methods, and Applications, Second Edition

2011-08-22T04:34:00.000-07:00

Given the explosive development of new molecular marker techniques over the last decade, newcomers and experts alike in the field of DNA fingerprinting will find an easy-to-follow guide to the multitude of techniques available in DNA Fingerprinting in Plants: Principles, Methods, and Applications, Second Edition. Along with step-by-step annotated protocols, the authors fully discuss the technical aspects and modifications of existing techniques, the influence of reaction components and conditions, and the analysis of the results. This second edition has been completely revised to address the exponential changes in the field since the first edition, focusing on PCR-based techniques but also including more sophisticated ones. The authors include numerous case studies to illustrate applications of the methods, more than 1600 references to the literature, and descriptions of reagent formulation, equipment, and computer programs used for evaluating molecular marker data. They compare the various methods, including the costs and benefits of each, helping readers determine which is best suited to a particular application. The well-rounded, cross-referenced, and unified nature of this book makes it intrinsically easier to follow than the edited, multi-authored books currently available. It is an absolute necessity on the lab bench of anyone involved in plant research, DNA profiling, and molecular markers.

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Forensic DNA Typing Protocols (Methods in Molecular Biology)

2011-08-22T04:25:00.000-07:00

by Angel Carracedo

A state-of-the-art collection of readily reproducible laboratory methods for DNA identity analysis, including Y chromosome haplotyping, mtDNA, and SNP typing. The book offers well-tested protocols for DNA quantification using real-time PCR on forensic samples and for the determination of the number of amelogenine gene copies. For forensic geneticists, there are readily reproducible methods for species identification, ancient DNA, and pharmacogenetics. Additional chapters address new applications in the forensic genetics lab, such a species identification or typing of CYP polymorphisms for the analysis of adverse to drugs.

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Fundamentals of Forensic DNA Typing

2011-08-22T04:18:00.000-07:00

John Butler

Ac emic P ss | ISBN : 0123749999 | 2009 | 519 pages | PDF | 2,8 MB

John Butler, bestselling author of Forensic DNA Typing, now applies his expertise on the subject of DNA analysis into an introductory textbook. Fundamentals of Forensic DNA Typing walks students step-by-step through the DNA analysis process beginning with collection of evidence at a crime scene to the statistical interpretation of the results.

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beginning programming with java for dummies e-book

2011-08-06T04:17:00.000-07:00

by Barry Burd

Covering everything from basic Java development concepts to the latest tools and techniques used in Java, this book will put would–be programmers on their way to Java mastery
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A Practical Guide to Designing for the Web e-book

2011-08-06T02:48:00.000-07:00

Mark Boulton

A Practical Guide to Designing for the Web aims to teach you techniques for designing your website using the principles of graphic design.Featuring five sections, each covering a core aspect of graphic design: Getting Started, Research, Typography, Colour, and Layout. Learn solid graphic design theory that you can simply apply to your designs, making the difference from a good design to a great one.

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Mastering Perl for Bioinformatics e-book

2011-08-05T10:38:00.000-07:00

by James Tisdall

“Mastering Perl for Bioinformatics covers the core Perl language and many of its module extensions, presenting them in the context of biological data and problems of pressing interest to the biological community. This book, along with Beginning Perl for Bioinformatics, forms a basic course in Perl programming. This second volume finishes the basic Perl tutorial material (references, complex data structures, object-oriented programming, use of modules--all presented in a biological context) and presents some advanced topics of considerable interest in bioinformatics. Biologists and computer scientists who have conquered the basics of Perl and are ready to move even further in their mastery of this versatile language will appreciate the author's well-balanced approach to applying Perl's analytical abilities to the field of bioinformatics. Full of practical examples and real-world biological problem solving, this book is a must for any reader wanting to move beyond beginner level Perl in bioinformatics.”

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Bioinformatics And Computational Biology Solutions Using R And Bioconductor e-book

2011-08-05T10:26:00.000-07:00

by Gentleman, Vincent Carey, Wolfgang Huber and Rafael Irizarry

"The book has several nice touches that readers will appreciate. First, the liberal use of color shows the full capabilities of Bioconductor pakages and brings the material to life. Second, color figures are dispersed throughout the text rather than being relegated to a central section of color plates. Third, the index indicates whether a term references a package, function or class. This book is an excellent resource... In summary, this book is a must have for any Bioconductor user." (J. Wade Davis, Journal of the American Statistical Association, Vol. 102, No. 477, 2007) "This book is solid evidence of the influence that quantitative researchers can have on biological investigations. Organized into separate chapters of shared authorship, the book provides a valuable overview of the impact that the authors and their colleagues have had on the analysis of genomic data." (R.W. Doerge, Biostatistics, December 2006) "This book provides an in-depth demonstration of the potential of the Bioconductor project, through a varied mixture of descriptions, figures and examples. a ] The book a ] is an exciting opportunity for researchers to learn directly from the software developers themselves. The range of material covered by the book is diverse and well structured. An abundance of fully worked case studies illustrate the methods in practice. a ] it should be a must for any researcher considering getting started with the software a ] ." (Rebecca Walls, Journal of Applied Statistics, Vol. 34 (3), 2007) Product Description Bioconductor is a widely used open source and open development software project for the analysis and comprehension of data arising from high-throughput experimentation in genomics and molecular biology. Bioconductor is rooted in the open source statistical computing environment R. This volume's coverage is broad and ranges across most of the key capabilities of the Bioconductor project, including importation and preprocessing of high-throughput data from microarray, proteomic, and flow cytometry platforms: Curation and delivery of biological metadata for use in statistical modeling and interpretation Statistical analysis of high-throughput data, including machine learning and visualization Modeling and visualization of graphs and networks The developers of the software, who are in many cases leading academic researchers, jointly authored chapters. All methods are illustrated with publicly available data, and a major section of the book is devoted to exposition of fully worked case studies. This book is more than a static collection of descriptive text, figures, and code examples that were run by the authors to produce the text; it is a dynamic document. Code underlying all of the computations that are shown is made available on a companion website, and readers can reproduce every number, figure, and table on their own computers.

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Instant Notes in Bioinformatics e-book

2011-08-04T03:02:00.000-07:00

Instant Notes in Bioinformatics, provides concise yet comprehensive coverage of bioinformatics at an undergraduate level, with easy access to the fundamentals in this complex field. All the important areas in bioinformatics are covered in a format which is ideal for learning and rapid revision and reference.

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Bioinformatics Programming Using Python e-book

2011-08-04T02:52:00.000-07:00

Paperback: 512 pages

Publisher: O'Reilly Media; 1 edition (December 23, 2009)ISBN-10: 059615450X ISBN-13: 978-0596154509

Powerful, flexible, and easy to use, Python is an ideal language for building software tools and applications for life scienceresearch and development. This unique book shows you how to program with Python, using code examples taken directly from bioinformatics. In a short time, you'll be using sophisticated techniques and Python modules that are particularly effective for bioinformatics programming.

Bioinformatics Programming Using Python is perfect for anyone involved with bioinformatics -- researchers, support staff, students, and software developers interested in writing bioinformatics applications. You'll find it useful whether you already use Python, write code in another language, or have no programming experience at all. It's an excellent self-instruction tool, as well as a handy reference when facing the challenges of real-life programming tasks.* Become familiar with Python's fundamentals, including ways to develop simple applications* Learn how to use Pythoz* Benefit from the "tips and traps" section in each chapter.

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Linux For Dummies 8th Edition e-book

2011-08-04T02:43:00.000-07:00

* Focusing on Fedora Core 6, this accessible guide shows newcomers how to create a full-featured Linux desktop setup that's comparable to a Windows system
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Ubuntu for Non-Geeks, 2nd Edition e-book

2011-08-04T02:37:00.000-07:00

Rickford Grant

This newbie's guide to Ubuntu - now updated for Ubuntu 7.04 (Feisty Fawn), the latest Ubuntu release, which puts the spotlight on multimedia enablement and desktop effects - lets readers learn by doing. Using immersion-learning techniques favored by language courses, step-by-step projects build upon earlier tutorial concepts, stimulating the brain and increasing the reader's understanding. Ubuntu for Non-Geeks, 2nd Edition covers all the topics likely to be of interest to an average desktop user. Inside, you'll learn to: - Download and install free applications, games, and utilities - Connect to the Internet and wireless networks - Configure your hardware, including printers, scanners, and removable storage devices - Watch DVDs, listen to music, and even sync your iPod - Download photos and videos from your digital camera, then edit and share them - Tackle more advanced tasks as soon as you're ready Full of tips, tricks, and helpful pointers, Ubuntu for Non-Geeks, 2nd Edition is a hands-on, project-based, take-it slow guidebook intended for those interested in-but nervous about-switching to the Linux operating system. Step-by-step projects build upon earlier tutorial concepts, helping you absorb and apply what you've learned.

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Bioinformatics: Sequence, Structure and Databanks e-book

2011-07-31T10:51:00.000-07:00

By Des Higgins, Willie Taylor

Publisher: Oxford University Press | 15-10-2000 | ISBN: 0199637903 | 249 pages | 20.8 Mb

Univ. College, Cork, Ireland. Thorough and authoritative account of current techniques and approaches in the field. Covers searching information on entire protein families as well as searching with single sequences. Also describes methods forcomputer networking for the molecular biologist.

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Bioinformatics: A Practical Approach e-book

2011-07-31T08:00:00.000-07:00

Shui Qing Ye

An emerging, ever-evolving branch of science, bioinformatics has paved the way for the explosive growth in the distribution of biological information to a variety of biological databases, including the National Center for Biotechnology Information. For growth to continue in this field, biologists must obtain basic computer skills while computer specialists must possess a fundamental understanding of biological problems. Bridging the gap between biology and computer science, Bioinformatics: A Practical Approach assimilates current bioinformatics knowledge and tools relevant to the omics age into one cohesive, concise, and self-contained volume.

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Analysis of Genes and Genomes e-book

2011-07-31T07:47:00.000-07:00

Richard J. Reece,

This beautifully illustrated textbook provides a clear guide to the tools and techniques of genetic engineering, gene cloning and molecular biology. All aspects of genetic engineering in the post-genomic era are covered, beginning with the basics of DNA structure and DNA metabolism. Using an example-driven approach, the fundamentals of creating mutations in DNA, cloning in bacteria, yeast, plants and animals are all clearly presented.

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Java for bioinformatics and biomedical applications e-book

2011-07-31T07:36:00.000-07:00

Harshawardhan Bal, Johnny Hujol

Java for Bioinformatics and Biomedical Applications describes the work of the U.S. National Cancer Institute (NCI, National Institutes of Health, U.S. Department of Health and Human Services) and a large number of cancer centers across the U.S. under the caBIG (cancer Biomedical Informatics Grid) program, as well as standard bioinformatics applications. The goal of NCI caBIG is to create a standards based, interoperable network of individuals, applications and data to enhance the pace of cancer research. CaBIG uses J2EE and open source standards for all software development work. This book examines the tools and technologies being developed under caBIG to meet the goal of eliminating suffering and death from cancer by 2015 as formulated by the former NCI Director, Dr. Andrew von Eschenbach.In doing so, it provides a vignette into the efforts of thousands of people molecular biologists, medical practitioners, software developers, to name a few - across the country to bring the promise of translational research to individuals with cancer.

From a software perspective, a functional approach is used to teach the Java platform and its features for enterprise-level application development. Under this approach, the various syntactical and operative elements of the language and any software libraries that have been used (for example, BioJava, Apache, etc.) are taught not in isolation but in the context of discrete definable research problems that enable the user to relate how the different parts of the language fit together in the big picture. All examples are derived from practical problems faced in biomedical/clinical data retrieval and analysis during routine bioinformatics and cancer research. Further, the book illustrates how individual bioinformatics applications (such as BLAST and Genscan) can be stitched together into a pipeline so that users can direct the output of one tool (for example, gene predictions using Genscan) to perform further analysis (say, homology searching using BLAST).

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Bioinformatics Research centers and Universities

2011-07-27T00:26:00.000-07:00

Advanced Biotechnology Center (CBA) Genoa, Italy
Analytical Chemistry at Umea University, Sweden
Ankara University Biotechnology Institute
Arizona Research Laboratories Univ. of Arizona
Australian National University Research School of Biological Sciences Bioinformatics Group
Bioinformatics Center, Institute for Chemical Research, Kyoto University
Broad Institute Research collaboration of MIT and Harvard and affiliated hospitals, and the Whitehead Institute.
Cabri Common Access to Biotechnological Resources and Information: aims to meet the need of European biotechnology research and development for high quality biological resources by providing common access for the user via the Internet to the resources and information of the providers within the project.
CCP11 Project Collaborative Computational Project 11 was established to foster the broad bioinformatics community and the UK research community in particular. Its purpose is to facilitate the transfer of knowledge and expertise through conferences, workshops, a newsletter and the use of the world wide web
Center for Integrated Genomics Univ. of British Columbia
Center for International Development (Harvard Univ.) Biotechnology policy discussions. Mailing list.
Centre for Photobiology and Photodynamic Therapy Developing the science of 'photodynamics' for the treatment of cancer and other diseases.
Chao Center for Industrial Pharmacy and Contract Manufacturing Developing drugs to treat diseases that mainly affect underprivileged populations, producing less-profitable drugs that are made in small volumes.
Cornell Center for Advanced Technology Biotechnology Program
Cornell Genomics Initiative
CPB Center for Pharmaceutical Technology
Cranfield University Biotechnology Centre An international centre of excellence in biotechnology for post-graduate education and industrially-related research.
CSUBIOWEB California State Univ. Biosciences Directory
Danish Centre for Human Genome Research
ETH Institute of Cell Biology
ExPASy Molecular Biology Server (Expert Protein Analysis System) proteomics server.
Flanders Interuniversity Institute for Biotechnology VIB
Fraunhofer Institute for Interfacial Engineering and Biotechnology Developing economically attractive and ecological solutions in the fields of biotechnology and environmental technology.
Fred Hutchinson Cancer Research Center Blocks WWW server: a service for biological sequence analysis.
George Mason Univ. Bioinformatics and computational biology.
gsf (German) National Research Center for Environment and Health.
Harvard Univ. Single port of entry to the Harvard Biomedical Community.
Human Genome Center, Institute of Medical Science, University of Tokyo
HyperCLDB Detailed descriptions of cell lines from European culture collections
IECRN The Inventory of Clinical Research Networks is one component of the NIH roadmap activity. The goal of the roadmap activity is to enhance the efficiency and productivity of the clinical research enterprise in conducting high quality clinical studies where multiple research questions are addressed.
IMB Institute for Molecular Biotechnology Germany
Indiana University Center for Genomics and Bioinformatics
Industrial Research Limited of New Zealand Biocatalysis and Enzyme Technology
Inst. of Arable Crops Research (UK)
Inst. of Molecular Biology and Biotechnology Foundation for Research and Technology, Heraklion, Crete, Greece
Inst.of Food and Agricultural Sciences, University of Florida
IST Istituto Nazionale per Ricerca suf Cancro
Jackson Laboratory Mouse genome databases; seminars and courses.
John Innes Centre International centre for research and training in plant and microbial science; generates and disseminates new knowledge, understanding and valuable intellectual property on selected plants and microbes including plant pathogens.
Johns Hopkins Univ. Bioinformatics
Joint Genome Institute - Department of Energy JGI brings four national laboratories, Lawrence Berkeley, Lawrence Livermore, Los Alamos, and Oak Ridge, and the Stanford Human Genome Center to bear on the frontiers of genome sequencing and related biology.
JPSL Joint ProteomicS Laboratory - Ludwig Institute for Cancer Research (Melbourne Branch) - The Walter and Eliza Hall Institute of Medical Research - links to databases.
Laboratory for Computational Genomics Rockefeller Univ.
Laboratory for Gene-Product Informatics National Institute of Genetics, Japan
Laurent Vuillard Protein refolding and NDSB WWW Page
Lewis-Sigler Institute for Integrative Genomics
Ludwig-Maximilians-UniversitSt Laboratory for Molecular Biology, Gene Center, Univ. of Munich
Lund University Department of Immunotechnology
MAGPIE Automated Genome Project Investigational Environment
Mankara Univ. Molecular genetics department
Midwest Research Institute An independent, not-for-profit, contract research organization with programs in national defense, health sciences, agriculture and food safety, engineering, environment, information technology, energy, biological sciences and analytical chemistry.
MIGAL Galilee Technological Center is an applied research institute, specializing in biotechnology, agriculture and environmental science.
National Center for Toxicogenomics NIEHS / NIH
National Institute of Genetics Japan
NBC National Biomanufacturing Centre England
Netherlands Bioinformatics Centre
Netherlands Proteomics Centre
Northwestern Univ. Medical School Basic Science departments and resources.
Organisms of Hawaii - Images Hawaiian Ecosystems at Risk Project - a remarkably inventive way to present information.
Oxford Univ Centre for the Molecular Sciences
Pasteur Inst. Microbiology - a searchable database of urls regarding biology (a web biology notebook), containing more than 2500 urls, classified according to: Resource Type, Species or Organism, and Discipline.
Princeton Univ.
Provasoli-Guillard National Center for Culture of Marine Phytoplankton
PSF The Protein Structure Factory - A common initiative of the German Human Genome Project (DHGP) and structural biologists from the Berlin area aimed at the broad-scale analysis of proteins; services for structural target validation, lead discovery and lead optimization.
Purdue Univ. Pharmaceutical technology and education center
QB3 The California Institute for Quantitative Biomedical Research is a cooperative effort among UC San Francisco, UC Berkeley, and UC Santa Cruz, and private industry; promotes and enables the integration of quantitative and biomedical sciences to advance our understanding of living systems at all levels of complexity.
RIKEN Genomic Sciences Center / Genome Exploration Research Group
Sanger Institute Genome research institute with many rich links.
SIB Swiss Institute of Bioinformatics
SimBioS Stanford Center for Biomedical Computation - Physics-Based Simulation of Biological Structures
South African National Bioinformatics Institute
Stanford Biochemistry: Brown Lab Build your own microarray and scanner.
Stanford Brutlag Bioinformatics Group
Stanford Genomic Resources Departments of Genetics and Biochemistry, and other associated programs and institutes.
Stanford Nanofabrication Facility
Technical University of Braunschweig Inst. of Pharmaceutical Technology
Technical University of Munich Physiology Department
The Center For Comparative Functional Genomics Univ. of Albany (New York, USA) Facilities and technical support to promote interdisciplinary research in genomics, bioinformatics, proteomics, microarray, mouse transgenesis, cell culture, FACS, and confocalimaging.
The Office of Biorenewables Programs (OBP) at Iowa State University Serves as a focal point for the activities of the bioeconomy initiative.
The RNAi Consortium TRC - Three-year public-private consortium to create a comprehensive library of gene inhibitors to be made available to the entire scientific community; initiated 2005.
The Scripps Research Institute A private, non-profit research organization engaged in basic biomedical science.
TIGR The Institute for Genomic Research
Tsinghua University Institute of Bioinformatics
Tufts Center for the Study of Drug Development Tufts University
Univ. College London Biochemistry and Molecular Biology
Univ. of Arizona Biotechnology Computing Facility
Univ. of Arkansas Biotechnology Arkansas
Univ. of Basel Biozentrum
Univ. of Birmingham Animal Cell Technology Group
Univ. of California at Los Angeles (UCLA) Faculty interest .
Univ. of California, San Francisco Cellular and Molecular Pharmacology
Univ. of Cambridge Department of Pathology, Divisions of Cellular Molecular Pathology, Immunology, Microbiology & Parasitology, Virology and Molecular Histopathology
Univ. of Florida Biotechnology Program
Univ. of Freiburg Institute for Biology
Univ. of Maine Program in Molecular Genetics and Cell Biology
Univ. of Manchester Biostatistics and Clinical Trials
Univ. of Maryland Functional Genomics and Molecular Medicine
Univ. of Maryland, Baltimore County Bioinformatics Research Center
Univ. of Minnesota Computational Biology Centers
Univ. of Minnesota Biochemistry, molecular biology and biophysics
Univ. of Murcia, Spain GENZ: Group of research on Enzymology
Univ. of Oklahoma Advanced Center for Genome Technology
Univ. of Texas at Austin Interdisciplinary Center for Molecular and Cellular Toxicology
Univ. of Texas Southwestern Medical Center Division of Cell and Molecular Biology
Univ. of Twente Institute for Biomedical Technology
Univ. of Ulm
Univ. of Vienna Theoretical Biochemisty Group, including the Vienna RNA Package for predicting and comparing RNA Secondary Structures
Univ. of Wales Aberystwtyth Quantitative Biology and Analytical Biotechnology
Univ. of Warwick Dept. of Biological Sciences (UK)
Univ. of Washington Bioengineering
Univ. of Washington Cytogenetics and genome project related tools.
Univ. of Wisconsin Programs in biotechnology
Univ. of Zurich Faculty of Veterinary Medicine Proteomics Center.
University of Illinois at Urbana-Champaign Theoretical and Computational Biophysics Group
Utah State Univ. Center for Integrated BioSystems
Virginia Tech Fralin Biotechnology Center
VMTC Victorian Microarray Technology Consortium (Australia)
Weizmann Inst Bioinformatics and Biological Computing
Whitehead Inst. for Biomedical Research Information on map and sequence releases, software and people at the Genome Center located at MIT.
Yale Univ Bioinformatics
Yale Univ. Biophysics and Biochemistry Center for Structural Biology
Zelinsky Institute of Organic Chemistry Russian Academy of Sciences

List of Bioinformatics Information Databases

2011-07-27T00:24:00.000-07:00

2can Bioinformatics Short and concise introductions to basic concepts in molecular and cell biology and bioinformatics. The main emphasis is placed on making it as easy as possible for the user to understand which tools and databases are available from the EBI and from sites belonging to its collaborators.
Addgene A non-profit organization dedicated to promoting sharing of plasmid constructs described in published literature. Addgene stores original plasmid samples submitted by scientists and distributes them for use in advancing life science research.
ALFRED Allele frequency database from the Kidd Lab at Yale Univ.
ANGIS Australian National Genomic Information Service provides access for biologists to a comprehensive system of bioinformatics software, databases, documentation, training and support, on a subscription basis.
Anti-Cancer Maps Public database with viewing tools (NCI).
ARP Antibody Resources Page
ATCC American Type Culture Collection
Atlas of Side-Chain and Main-Chain Hydrogen Bonding is available for biomolecular modellers (UK)
AtlasInfo Bioinformatics System for AtlasTM cDNA Expression Arrays
Bacterial Names with Standing in Nomenclature
Base4 Bioinformatics Integrated systems solutions for biotechnology and pharmaceutical development.
BCM Search Launcher Baylor Human Genome Center
Berkeley Drosophila Genome Project
BGEM Mousebrain Gene Expression Map database at St. Jude
BIND Biomolecular Interaction Network Database
BIOBASE Specialized biological databases, mainly from the field of molecular biology, including the TRANSFAC database on transcription factors, their genomic binding sites and their general binding profiles.
BioCarta Proteomics marketplace and resource center.
BioChipNet More than 13.000 records on companies and institutions involved in microarray technology microarray-relevant publications, comprehensive glossary, upcoming biochip-related meetings and conferences, and hyper to public databases.
bioinf.org.uk Bioinformatics Web Site of Dr. Andrew C.R. Martin.
Bioinformatic Harvester Caches and cross-links public bioinformatic databases and prediction servers to provide fast access to protein specific bioinformatic information. Presently the following databases and servers are implemented: Uniprot/SWISSprot, ensEMBL, BLAST (NCBI), SOURCE, SMART, STRING, PSORT2, CDART, UniGene and SOSUI.
Bioinformatics Club Bioinformatics resource providing access to widely used bioinformatics databases and tools.
Bioinformatics.net Directory of bioinformatics and molecular biology.
Bioinformatics.org News and information. Links to online computational tools.
Biomax Informatics Bioinformatics software.
BioNavigator Tools to manage and analyze the large amounts of data generated by bioscience research.
Biosciences databases.
BioSimGrid A distributed database for biomolecular simulations.
BioTX Automation Design and construction of complex mechanical components; automated liquid handling for the life science laboratory; USGRD database of federal grants awarded.
BioWisdom Ontologies and related tools focused on drug discovery. .
BRENDA Comprehensive enzyme information system.
California Digital Library Searchlight ... searches databases.
CCP11 Project Collaborative Computational Project 11 was established to foster the broad bioinformatics community and the UK research community in particular. Its purpose is to facilitate the transfer of knowledge and expertise through conferences, workshops, a newsletter and the use of the world wide web
Chartsbank.com A market research portal with an extensive pharmaceutical pipeline database.
Chmoogle Access to millions of public domain chemical structures and information about them; fast substructure searches.
CKAAPs DB Contains the analysis of conserved amino acid positions based on protein structural alignment from CE and FSSP; provides an analysis of conserved key positions in protein structures, with implications in structural integrity, functional site or protein engineering studies.
Clinical Bioinformatics Ontology "Existing medical vocabularies lack rich terms to describe findings generated by molecular diagnostic and cytogenetic techniques. Likewise, bioinformatics resources were not designed to support the needs of the clinical community. The Clinical Bioinformatics Ontology™ (CBO) was initiated to address these gaps and covers the areas of molecular genetics, molecular pathology, cytogenetics and infectious disease."
CPBP The Carcinogenic Potency Database
CSH Protocols Cold Spring Harbor - Methods from MolecularCloning.com along with selected protocols from many of our best-selling manuals, such as Cells and Antibodies, as well as protocols from Cold Spring Harbor’s renowned on-site courses. In addition, new cutting-edge protocols submitted by and commissioned from laboratories worldwide.
Database of Macromolecular Movements Includes associated tools for geometric analysis.
DataEdge Information to assist in pharmaceutical development, clinical trials and related activities.
DBCAT The catalog of databases.
DBSubLoc Database of Protein Subcellular Localization at Institute of Bioinformatics, Tsinghua University.
Deltagen Bioinformatics - Library of functional information about mammalian gene families with potential relevance to small molecule drug discovery; Gene knockout and conditional knockout programs; discover and identify the functional role of rare or novel secreted proteins.
Derwent GENSEQ Information on nucleic and amino acid sequences from worldwide patents.
Developmental Therapeutics Program Resources for drug development, including compound libraries, cell lines, screening, and databases.
DNA Data Bank of Japan
DOE U.S. Department of Energy-sponsored human genome research projects.
DrugBank Bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, pathway) information. Contains nearly 4100 drug entries including >700 FDA-approved small molecule drugs, 110 FDA-approved biotech (protein/peptide) drugs, >100 nutraceuticals and >3200 experimental drugs. More than 15,000 protein (i.e. drug target) sequences are linked to these drug entries. Each DrugCard entry contains more than 80 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data. Users may query DrugBank in any number of ways.
DSDBASE Database on disulphide bonds in proteins that provides information on native disulphides and those which are stereochemically possible between pairs of residues in a protein.
EBI European Bioinformatics Institute
ELM The Eukaryotic Linear Motif resource for predicting functional sites (described by linear motifs) in eukarytic proteins.
Elsevier Scientific BioMedDirect Integrated group of products and services addresses the needs of the biomedical research community and corporate healthcare markets, providing comprehensive navigation and linking to full text.
EMBL A service for sequence analysis, and structure prediction
EMBL European Molecular Biology Laboratory centre for research and services in bioinformatics. The Institute manages databases of biological data including nucleic acid, protein sequences and macromolecular structures.
eMOTIF Nucleic acid database.
Environmental Mutagen Society
ExPASy Molecular Biology
First Genetic Trust Secure, web-based technology system for handling and analyzing medical and genetic information.
FishBase Global Information System on Fishes
GATC GmbH Sequencing service.
GBF Research Group for Bioinformatics The focus of the GBF research group bioinformatics are regulatory genomic signals and regions, in particular those that govern transcriptional control.
gdb The Genome Database
GeMCRIS NIH Genetic Modification Clinical Research Information System, a comprehensive information resource and analytical tool for scientists, research participants, institutional oversight committees, sponsors, federal officials, and others with an interest in human gene transfer research.
Gene and Protein Synonym Database Comprehensive database of gene and protein name synonyms. This authoritative thesaurus, published by PharmaDM, has been compiled in cooperation with SIB (the publishers of Swiss-Prot and ExPASy), OFAI, the University of Manchester, and others.
Gene Ontology Project A controlled vocabulary to describe gene and gene product attributes in any organism.
GeneGo Develops tools for integration and systems level analysis of high-throughput experimental data in human biology and medicinal chemistry. Includes MetaBase, a manually curated database on human biology in norm and diseases
Genetics at Yahoo via Yahoo
Genetics Education Center University of Kansas Medical Center
Genetics Home Reference The National Library of Medicine's web site for consumer information about genetic conditions and the genes or chromosomes responsible for those conditions.
Genetics Section of the WWW Virtual Library
Genolist Genome Browser Useful links to genome sequence sites.
Genome@home Stanford Univ. grid computing project.
GenomeNet Japanese network of database and computational services for genome research and related research areas in molecular and cellular biology.
Genomics and Bioinformatics Group NIH Bioinformatic program packages, microarray data analysis information, and molecular databases for genomic and proteomic research.
GermOnline A cross-species community annotation knowledgebase that provides microarray data relevant for the mitotic and meiotic cell cycle as well as gametogenesis. Importantly, GermOnline also integrates knowledge about genes important for sexual reproduction that is contributed and updated by members of the scientific community in collaboration with professional curators.
Globin Gene Server Data and tools for studying the function of DNA sequences, with an emphasis on those involved in the production of hemoglobin.
GTOP Database Genomes TO Protein structures and functions; constructed by the Laboratory for Gene-Product Informatics at the National Institute of Genetics
HCV Database Hepatitis C
HGMD Human gene mutation database
HGSC Human Genome Sequencing Center
HGVbase Human Genome Variation database (formerly.HGBASE)
H-Invitational Database H-Invitational Database (H-InvDB) is a human gene database, with integrative annotation of 41,118 full-length cDNA clones currently available from six high throughput cDNA sequencing projects. (July 2004)
HIV Sequence Database
Human Genome Mapping Project (HGMP) Resource Centre (UK) A rich source of information and .
Human Genome Project
Human Genome Variation Society Locus Specific Mutation Databases Out of date but has some good to other variation databases.
Human Serum Proteome Human serum proteomic database to provide a reference resource to facilitate and direct future investigations of the vast archive of pathophysiological content in serum.
HyperCLDB Detailed descriptions of cell lines from European culture collections
IFPMA Clinical Trials Portal International Federation of Pharmaceutical Manufacturers and Associations clinical trials registry
IMGT The international ImMunoGeneTics database, is an integrated database specialising in Immunoglobulins (Ig), T-cell receptors (TcR) and Major Histocompatibility Complex (MHC) molecules of all species.
IncyteGenomics Genomic information-based tools to accelerate the discovery and development of new diagnostic and therapeutic products.
Informatics Online "Healthcare research and analytic community designed to meet the present and future needs of healthcare researchers and market economics professionals."
Inpharmatica Biopendium, a resource of protein structure and function information that enables the identification of distantly related proteins to identify high quality drugable targets and predict the structure of interacting ligands, facilitating the rational design of lead compounds.
InterPro Resource for whole genome analysis.
ISI A database publisher with a focus on Web-based products that offer scholarly research information in the sciences, social sciences, and arts & humanities, including BioSciences Citation Index, Chem Sciences Citation Index, and Clinical Medicine Citation Index.
KEGG Kyoto Encyclopedia of Genes and Genomics
Leadscope Chemoinformatics software, databases created with the U.S. FDA along with prediction capabilities.
Library of Protein Family Cores Taking the structural alignments of protein families and computed average core structures for each family. The core structures can be divided into residues with low spatial variation and those with high spatial variation. Amino acids with low spatial variance occupy essentially the same relative position in all family members. This library is useful for building models, threading, and exploratory analysis. It is also a useful mechanism for summarizing variability in NMR structures.
Mammary Transgene Database The Molecular Biology Computational Resource, Baylor College of Medicine, Houston, Texas
MDL Information Systems Discovery informatics for the life sciences and chemistry in industry and academia; a wide variety of software for discovery informatics, high throughput chemistry, biological data management, content browsing and data analysis, chemical sourcing and logistics, bioactivity databases, synthetic methodology, patents, etc.
MedDRA MSSO MedDRA Maintenance and Support Services
MedGene Database Harvard's database uses an automated approach to assemble disease-gene co-citation matrices from the titles, abstracts and MESH terms of over 11 million Medline records and normalizes these gene-disease relationships into rank order.
MHC Haplotype Project A framework and resource for association studies of all MHC linked diseases.
MICROMEDEX Knowledgebases for healthcare, safety and the environment.
mips Munich Information Center for Protein Sequences.
Molecular Toolbox Sidney Morris' collection of databases and utilities.
Mosquito Genomics WWW Server
NAPRALERT A relational database of all natural products, including ethnomedical information, pharmacological/biochemical information of extracts of organisms in vitro, in situ, in vivo, in humans (case reports, non-clinical trials) and clinical studies. Similar information is available for secondary metabolites from natural sources.
NCBI National Center for Biotechnology Information (USA) Excellent to databases. BLAST NCBI GenBank
NCBI Trace Archive Developed to store the raw data underlying all of the sequence generated by the genome project.
NCTR National Center for Toxicological Research, US FDA, Center for Toxicoinformatics
NDB Nucleic Acid Database at Rutgers
NHGRI U.S. National Human Genome Research Institute (U.S.) Software available for download, including ArrayDB, ComboScreen, eSAGE, GeneMachine, G.A.S.P., NHGRI::Blastall.pm perl module, SOOP, WebBlast andothers.
NIH Office of Dietary Supplements Extensive dietray supplements information.
NOAA Molecular Biology Server / Bioinformatics US Dept Commerce/NOAA/NMFS/NWFSC
Oak Ridge National Laboratory
Ontario Centre for Genomic Computing OCGC
PCR .com Web guide of polymerase chain reaction technique.
PDB RCSB Protein Data Bank, worldwide repository for the processing and distribution of 3-D biological macromolecular structure data.
PDB Protein Data Bank - tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease.
PDBbind Database The public-accessible PDBbind database is designed to provide a collection of experimentally measured binding affinity data (Kd, Ki, and IC50) exclusively for the protein-ligand complexes available in the Protein Data Bank (PDB). Most of the binding affinity data (>95%) in the PDBbind database were collected from original references.
Pfam Large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families.
Phenomic Database A multi-organism phenotype-genotype database including human, mouse, fruit fly, C.elegans, and other model organisms. The inclusion of gene indexes (NCBI Gene) and orthologues (same gene in different organisms) from HomoloGene in this database allows the user to compare phenotypes of a gene over many organisms simultaneously.
PhRMA Bioinformatics Industry information, meetings, news.
pkr Protein Kinase Resource
PredictProtein
ProClass Database Non-redundant protein database organized according to family relationships as defined collectively by ProSite patterns and PIR superfamilies.
ProDom Comprehensive set of protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases.
Profile Scan Server Motif scanning in protein sequences.
PROLYSIS A Web resource for those interested in proteases and their natural or synthetic inhibitors; contains informations of general interest as well as useful to other Internet resources.
PROSITE Database of protein families and domains; consists of biologically significant sites, patterns and profiles that help to reliably identify to which known protein family (if any) a new sequence belongs.
Protein Information Resource (PIR) In collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the most comprehensive and expertly annotated protein sequence database in the public domain; contains about 2000,000 non-redundant protein sequences.
ProtoNet Automatic hierarchical classification of proteins.
PubChem Provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative
PubGene Data-mining software that searches through the millions of biology-related papers published for the names of all human genes; articles are then searched for the occurrence of gene pairs.
PubGene Norway Mirror for PubGene
Reactome A collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology
repairGenes Information about DNA repair genes and a useful resource for research on DNA repair.
RNA Structure Database RNABase
SBASE Online protein domain library.
SciFinder A service of the American Chemical Society.
SIB Swiss Institute of Bioinformatics
Sigma-Aldrich Library of Rare Chemicals
SIS (EVCAM) Scientific Information Service on advanced alternative methods to animal experiments in biomedical sciences; a database of the European Commission.
Skeletal Muscle Gene Expression Database A centralized source of up to date information regarding the effects of changes in contractile activity on the profile of genes expressed in skeletal muscle.
SNP Consortium
Stanford Microarray Database SMD stores raw and normalized data from microarray experiments, as well as their corresponding image files. In addition, SMD provides interfaces for data retrieval, analysis and visualization. Data is released to the public at the researcher's discretion or upon publication.
STD Sequence Databases Specialized databases that are an expansion of the human papillomavirus project funded by the National Institute of Allergy and Infectious Diseases (NIAID).
STN Connects scientists and engineers to the world's most complete and authoritative databases; includes AnaVist interactive analysis and visualization software that offers a variety of ways to analyze search results from scientific literature and patents as well as visualize patterns and trends in the research.
STRBase Short Tandem Repeat DNA Internet Database at NIST
SURFACE Database containing the results of a large-scale protein annotation and local structural comparison project; includes visulaization tools.
SWICZ Swiss-Czech proteomics web server created by the Laboratory of Bioinformatics, Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, and Division of Molecular Microbiology, Biozentrum, University of Basel. The aim of this server is presentation of developmental proteomics databases of Caulobacter crescentus, Streptomyces coelicolor and Streptomyces granaticolor.
TAP The Yeast TAP Project is aimed at elucidating the entire network of protein-protein interactions in a model eukaryotic organism, namely the yeast Saccharomyces cerevisiae,
The Human Genome Wellcome Trust public information site.
TIRC Toxicology Information Response Center
TreeBASE A relational database of phylogenetic information.
UBC Bioinformatics Center Univ. of British Columbia, Canada
UMC Products WHO Drug Dictionary Enhanced, WHO Herbal Dictionary, international drug safty data, WHO-ART adverse reaction terminology, training in the use of WHO Drug Dictionaries.
Virtual Genome Center
Virus databases on-line Research School of Biological Sciences, The Australian National University
WebMol by Dirk Walther (UCSF) A Java PDB (Brookhaven Protein Data Bank) viewer.
Wiley's Scientific, Technical, and Medical Databases A range of fee-based databases, including mass spectrometry.
WIT What-Is-There? A www-based system to support the curation of function assignments made to genes and the development of metabolic models.
wwPDB Worldwide Protein Data Bank - consists of three member organizations that act as deposition, data processing and distribution centers for PDB data. The founding members are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan). The mission of the wwPDB is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community.
Zebrafish Information Network

Make your own Supercomputer - Clustering tutorial

2011-07-26T01:35:00.000-07:00

An extensive tutorial on Linux clustering, steps for building a cluster and brief description of MPI.

Clustering is the use of multiple computers, typically PCs or UNIX workstations, multiple storage devices, and redundant interconnections, to form what appears to users as a single highly available system. Cluster computing can be used for load balancing as well as for high availability. It is used as a relatively low-cost form of parallel processing machine for scientific and other applications that lend themselves to parallel operations.

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Intelligent Bioinformatics: The Application of Artificial Intelligence techniques to bioinformatics Problems e-book

2011-07-25T10:16:00.000-07:00

Bioinformatics is contributing to some of the most important advances in medicine and biology. At the forefront of this exciting new subject are techniques known as artificial intelligence which are inspired by the way in which nature solves the problems it faces. This book provides a unique insight into the complex problems of bioinformatics and the innovative solutions which make up intelligent bioinformatics Intelligent Bioinformatics requires only rudimentary knowledge of biology, bioinformatics or computer science and is aimed at interested readers regardless of discipline. Three introductory chapters on biology, bioinformatics and the complexities of search and optimisation equip the reader with the necessary knowledge to proceed through the remaining eight chapters, each of which is dedicated to an intelligent technique in bioinformatics. The book also contains many links to software and information available on the internet, in academic journals and beyond, making it an indispensable reference for the 'intelligent bioinformatician'. Intelligent Bioinformaticswill appeal to all postgraduate students and researchers in bioinformatics and genomics as well as to computer scientists interested in these disciplines, and all natural scientists with large data sets to analyse.

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Structural Bioinformatics e-book

2011-07-25T10:11:00.002-07:00

Philip E. Bourne, Helge Weissig

The emerging discipline of structural bioinformatics comprises the development of computational technologies for methods of storage, retrieval, and analysis of the three-dimensional structure of biological macromolecules. Edited by Philip Bourne and Helge Weissig, this groundbreaking text provides a thorough understanding of the theories, associated algorithms, resources, and tools used in structural bioinformatics.

Structural Bioinformatics begins with chapters on the fundamentals of protein structure, DNA/RNA structure, carbohydrates, and techniques including X-ray crystallography, NMR, cryo-electron microscopy, and molecular visualization. The next section addresses data representation and databases, followed by information on structure classification of proteins (SCOP) and class, architecture, topology, and homology (CATH) classification. Later chapters cover structure-function assignment, protein interactions, and proteins as drug targets. Structural Bioinformatics also:

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