Data Simplification: Identifiers
Over the next few weeks, I will be writing on topics related to my latest book, Data Simplification: Taming Information With Open Source Tools (release date March 23, 2016). I hope I can convince you that this is a book worth reading. Blog readers can use the discount code: COMP315 for a 30% discount, at checkout. "I always wanted to be somebody, but now I realize I should have been more specific." -Lily Tomlin An object identifier is anything associated with the object that persists throughout the life of the object and that is unique to the object (i.e., does not belong to any other object). Everyone is familiar with...
Source: Specified Life - March 6, 2016 Category: Information Technology Tags: complexity computer science data analysis data repurposing data simplification data wrangling identifiers information science simplifying data taming data Source Type: blogs
Data Simplification: Hitting the Complexity Barrier
Conclusions have no value until they are independently validated. Anyone who attempts to stay current in the sciences soon learns that much of the published literature is irreproducible (8); and that almost anything published today might be retracted tomorrow. This appalling truth applies to some of the most respected and trusted laboratories in the world (9), (10), (11), (12), (13), (14), (15), (16). Those of us who have been involved in assessing the rate of progress in disease research are painfully aware of the numerous reports indicating a general slowdown in medical progress (17), (18), (19), (20), (21), (22), (23...
Source: Specified Life - March 5, 2016 Category: Information Technology Tags: complexity computer science data analysis data repurposing data simplification data wrangling information science simplifying data taming data Source Type: blogs
Data Simplification: Chapter Synapses
Over the next few weeks, I will be blogging on topics selected from Data Simplification: Taming Information With Open Source Tools. Those of you who are computer-oriented know that data analysis typically takes much less time and effort than data preparation. Moreover, if you make a mistake in your data analysis, you can often just repeat the process, using different tools, or a fresh approach to your original question. As long as the data is prepared properly, you and your colleagues can re-analyze your data to your heart's content. Contrariwise, if your data is not prepared in a manner that supports sensible analysis, t...
Source: Specified Life - March 4, 2016 Category: Information Technology Tags: computer science data analysis data repurposing data simplification data wrangling information science simplifying data taming data Source Type: blogs
Data Simplification: Contents
On March 23, my book, Data Simplification: Taming Information With Open Source Tools, will be published. Here is a preview of the contents: TABLE OF CONTENTSChapter 0. Preface References for Preface Glossary for PrefaceChapter 1. The Simple Life Section 1.1. Simplification drives scientific progress Section 1.2. The human mind is a simplifying machine Section 1.3. Simplification in Nature Section 1.4. The Complexity Barrier Section 1.5. Getting ready Open Source Tools for Chapter 1 Perl Python Ruby Text Editors OpenOffice Command line utilities Cygwin, Linux emulation for ...
Source: Specified Life - March 3, 2016 Category: Information Technology Tags: computer science data analysis data repurposing data simplification data wrangling information science simplifying data taming data Source Type: blogs
Data Simplification: Why Bother?
Conclusions that cannot be validated have no scientific value. 3) Data simplification is not simple. There is something self-defeating about the term, "data simplification". The term seems to imply a dumbing down process wherein naturally complex concepts are presented in a manner that is palatable to marginally competent scientists. Nothing can be further from the truth. Creating overly complex data has always been the default option for lazy-minded or cavalier scientists who lacked the will or the talent to produce a simple, well-organized, and well-annotated collection of data. The act of data simplification will...
Source: Specified Life - March 2, 2016 Category: Information Technology Tags: computer science data analysis data repurposing data simplification data wrangling information science simplifying data taming data Source Type: blogs
Data Simplification: Book Announcement
On March 23, my book, Data Simplification: Taming Information With Open Source Tools, will be published. Those of you who are computer-oriented know that data analysis typically takes much less time and effort than data preparation. Furthermore, if you make a mistake in your data analysis, you can often just repeat the process, using different tools, or a fresh approach to your original question. As long as the data is prepared properly, you and your colleagues can re-analyze your data to your heart's content. Contrariwise, if your data is not prepared in a manner that supports sensible analysis, there's little you can ...
Source: Specified Life - March 1, 2016 Category: Information Technology Tags: announcement data analysis data repurposing data simplification Source Type: blogs
Rare Disease Day is Here!
It's finally come; the rare day that comes every four years, Rare Disease Day. For the past several weeks, leading up to February 29, I've been blogging about rare diseases. The basic theme of all my blogs is that the rarity of rare diseases is not a numeric accident. The rare diseases form a distinct class of diseases having a distinct set of unifying biological properties that distinguish them from common diseases. In the past 30 years, most of the great advances of medicine have been in the realm of the rare diseases; not the common diseases. In many cases, progress in the common diseases has come as a secondary ga...
Source: Specified Life - February 29, 2016 Category: Information Technology Tags: common diseases complex diseases funding for rare disease research medical research orphan diseases orphan drugs rare disease day zebra diseases Source Type: blogs
Rare Diseases Hiding Among Common Diseases
In June, 2014, my book, entitled Rare Diseases and Orphan Drugs: Keys to Understanding and Treating the Common Diseases was published by Elsevier. The book builds the argument that our best chance of curing the common diseases will come from studying and curing the rare diseases. Here is an excerpt from Chapter 12:It is easy to find cases wherein a rare disease accounts for a somewhat uncommon clinical presentation of a common disease. 12.1.2 Rule—Uncommon presentations of common diseases are sometimes rare diseases, camouflaged by a common clinical phenotype. Brief Rationale—Common diseases tend to occur with a char...
Source: Specified Life - July 18, 2014 Category: Pathologists Tags: common disease cryptic disease disease genetics genetics of common diseases genetics of complex disease orphan disease orphan drugs rare disease subsets of disease Source Type: blogs
Pareto's Principle and Long-Tailed Distribution Curves
In June, 2014, my book, entitled Rare Diseases and Orphan Drugs: Keys to Understanding and Treating the Common Diseases was published by Elsevier. The book builds the argument that our best chance of curing the common diseases will come from studying and curing the rare diseases. The book has an extensive glossary, that explains the meaning and relevance of medical terms appearing throughout the chapters. The glossary can be read as a stand-along document. Here is an example of one term, "Pareto's Principle", excerpted from the glossary.Pareto’s principle - Also known as the 80/20 rule, Pareto’s principle holds th...
Source: Specified Life - July 17, 2014 Category: Pathologists Tags: 80/20 rule common disease data analysis glossary orphan disease orphan drugs rare disease statistics Source Type: blogs
Relationship between Hamartoma and Cancer
In June, 2014, my book, entitled Rare Diseases and Orphan Drugs: Keys to Understanding and Treating the Common Diseases was published by Elsevier. The book builds the argument that our best chance of curing the common diseases will come from studying and curing the rare diseases. The book has an extensive glossary, that explains the meaning and relevance of medical terms appearing throughout the chapters. The glossary can be read as a stand-along document. Here is an example of one term, "hamartoma", excerpted from the glossary.Hamartoma - Hamartomas are benign tumors that occupy a peculiar zone lying between neoplasi...
Source: Specified Life - July 15, 2014 Category: Pathologists Tags: cancer types carcinogenesis common cancers disease genes genetic disease hyperplasia orphan disease orphan drugs rare cancers rare disease tissue overgrowth tumor biology tumor types Source Type: blogs
Aneuploidy and Carcinogenesis
In June, 2014, my book, entitled Rare Diseases and Orphan Drugs: Keys to Understanding and Treating the Common Diseases was published by Elsevier. The book builds the argument that our best chance of curing the common diseases will come from studying and curing the rare diseases. The book has an extensive glossary, that explains the meaning and relevance of medical terms appearing throughout the chapters. The glossary can be read as a stand-along document. Here is an example of one term, "aneuploidy", excerpted from the glossary.Aneuploidy - The presence of an abnormal number of chromosomes (for the species) in a cell...
Source: Specified Life - July 15, 2014 Category: Pathologists Tags: aneuploidy cancer types carcinogenesis common cancers common disease cytogenetics glossary orphan disease orphan drugs rare cancers rare disease tumor biology tumor types types of cancer Source Type: blogs
Most Types of Cancer are Rare Cancers
In June, 2014, my book, entitled Rare Diseases and Orphan Drugs: Keys to Understanding and Treating the Common Diseases was published by Elsevier. The book builds the argument that our best chance of curing the common diseases will come from studying and curing the rare diseases. Here is an excerpt from Chapter 8:There are about 6000 types of cancer that have been assigned names by pathologists [4–6]. About a dozen of these cancers are common diseases. The remaining cancers (i.e., about 6000 entities) comfortably qualify as “rare” under U.S. Public Law 107-280, the Rare Diseases Act of 2002 [7]. Consequently, healt...
Source: Specified Life - July 14, 2014 Category: Pathologists Tags: cancer types common cancers common disease orphan disease orphan drugs rare cancers rare disease tumor biology tumor types types of cancer Source Type: blogs
Clinical trial failures: help from the Rare Diseases
In June, 2014, my book, entitled Rare Diseases and Orphan Drugs: Keys to Understanding and Treating the Common Diseases was published by Elsevier. The book builds the argument that our best chance of curing the common diseases will come from studying and curing the rare diseases. For a variety of reasons, clinical trials for rare diseases tend to have much greater likelihood of success than clinical trials on common diseases. Moreover, treatments developed for the rare diseases will almost always find some value in the treatment of one or more common diseases [a major theme discussed developed in the book]. Here is a ...
Source: Specified Life - July 13, 2014 Category: Pathologists Tags: ancillary studies clinical trials common disease complex disease orphan disease orphan drugs rare disease reproducibility statistical significance trial design Source Type: blogs
Treating precancers reduces breast cancer deaths
Breast cancer deaths rose through the '70s and '80s, but declined in the '90s. For nearly the past 20 years, American women have had about a 2% annual drop in the breast cancer death rate.Here is the mortality graph provided by the National Cancer Institutes SEER (Surveillance, Epidemiology and End Results) program.Though nobody wants to take the blame for the rise in breast cancer deaths in the '70s and '80s, lots of people want credit for the fall of breast cancer deaths that began in the '90s. Was it due to a reduction to the exposure of carcinogens, or to better treatment, or to earlier diagnosis? The fall in breast...
Source: Specified Life - July 13, 2014 Category: Pathologists Tags: cancer prevention cancer treatment early treatment precancer precancer treatment preneoplasia preneoplastic Source Type: blogs
Causality: Single Gene Disorders Can be Biologically Complex
In June, 2014, my book, entitled Rare Diseases and Orphan Drugs: Keys to Understanding and Treating the Common Diseases was published by Elsevier. The book builds the argument that our best chance of curing the common diseases will come from studying and curing the rare diseases. One of the points discussed in the book is disease causation, and how we often fool ourselves into thinking that we understand how a disease develops, simply because we can name the gene or agent that precipitates the disease. A gene may code for a single protein, but complex genetic and epigenetic conditions will effect the individual's respo...
Source: Specified Life - July 11, 2014 Category: Pathologists Tags: causality cause of disease common disease complex disease diabetes disease causation HGPRT Lesch-Nyhan monogenic disease orphan disease orphan drugs pathogenesis rare disease Source Type: blogs
