Thursday, December 31, 2009

Welcome 2010!

According to Bill Vaughan, an optimist stays up until midnight to see the new year in. A pessimist stays up to make sure the old year leaves.

Goodbuy 2009 was more frequently twitted as 2010 was sweeping across the globe, but there were no more pessimists left shortly after 2010 arrived on the islands of Western Hemisphere.
2009 was a year to remember but not repeat . Everyone hopes for a better year, so "Happy New Year"will continue to be a trending topic for a while - even if not among the top 10.

Wellcome 2010!

Monday, December 21, 2009

The Power Of Visualization

Things change, but we don't always understand how. Networks and clustering methods help to uncover changes in complex large-scale systems, but more sophisticated approaches are needed to distinguish between real trends and noisy data, between meaningful structural changes and random fluctuations. A recent PlosOne article demonstrated how bootstrap resampling accompanied by significance clustering provides a solution to this problem. The figure on the right illustrates major shifts in the structure of scientific research, showing how neuroscience emerged from an interdisciplinary specialty to a mature and stand-alone discipline.
The figure was generated by (i) clustering the original networks observed at each time point; (ii) generating and clustering the bootstrap replicate networks for each time point; (iii) determining significance of the clustering for at each time point; and finally to reveal stories in the network data and connect the changes between time points (iv) generating an alluvial diagram.

The technology used to generate biological networks is not and can't be very accurate, "medium" accuracy -for yeast two-hybrid screening of protein-protein interactions, as an example, - is on the order of 50% false positives. A recent article in PNAS titled, "Missing and Spurious Interactions and the Reconstruction of Complex Networks" by Guimera et al. outlines a method to accurately analyze different types of complex networks. It strongly relies on the fact that the nodes in networks can be organized into groups. Group membership governs which nodes can interact.

Many other simpler data visualization tools and methods exist suitable to other specific data-rich applications. IBM's Many Eyes site provides a variety of ways to analyze text, maps, trends and relationships among data points.

Bubble diagrams (also known as bubble charts and spray diagrams) are centered around one (like mind maps) or more concepts. They can then be used to compare and contrast concepts, and identify the common ground and the areas of difference. Diagramic builds such diagrams from spreadsheets and text files.

World Wibe Web makes huge quantities of information readily available."How do you take a big collection of things and make sense out of it?" asks Gary Flake, founder and director of Microsoft Live Labs designing experimental Web tools. The lab's answer to this question is Pivot, a tool recently released to the public - see a demonstration Flake gave at the TED conference in Long Beach, CA.

UI designer Theresa Neil highlights these 28 tools for creating graphs, Gantt charts, diagrammers, calendars/schedulers, gauges, mapping, pivot tables, OLAP cubes, and sparklines, in Flash, Flex, Ajax or Silverlight.
This platform is a pure javascript application framework for creating real-time collaborative applications that run in the browser.

AnyChart is a flexible Flash based solution that allows you to create interactive and great looking flash charts.

Axiis is a Data Visualization Framework for Flex. It has been designed to be a concise, expressive, and modular framework that let developers and designers create compelling data visualization solutions.

BirdEye is a community project to advance the design and development of a comprehensive open source information visualization and visual analytics library for Adobe Flex. The actionscript-based library enables users to create multi-dimensional data visualization interfaces for the analysis and presentation of information.

Degrafa is a declarative graphics framework for creating rich user interfaces, data visualization, mapping, graphics editing and more.

DojoX Data Chart
An addition in the Dojo 1.3 release is the new dojox.charting class. Its primary purpose is to make connecting a chart to a Data Store a simple process.

If you need to visualize thousands or millions of points of data, check this out. Very well designed and can be navigated with the keyboard or mouse. There's a Javascript API, a Google Visualization API or try it as a Google Gadget on Google Spreadsheets, iGoogle, or Open Social.

Dundas provides a wide range of data visualization solutions for Microsoft technologies. They offer a number of data visualization tools including: Chart, Gauge, Map and Calendar for .net and Dashboards for Silverlight.


Ext JS is a cross-browser JavaScript library for building rich internet applications. It also includes charts.

Flex has built in chart controls: area, bar, bubble, candlestick, column, HLOCC, Line, Pie, Plot.
Flex uses FXG, a graphical interchange format developed by Adobe and is similar in many ways to SVG. Nice article here by James Whittaker looking at FXG and Degrafa. See quick tutorial and article on Creating Visual Experiences with Flex 3.0.

FlexMonster Pivot Table and Charts
Flexmonster provides Pivot table Flex/Flash components rich internet application (RIA) development services.

Animated flash charts for web apps.

Google Chart API

The Google Chart API lets you dynamically generate charts.

gRaphaël is a Javascript library to help you create stunning charts on your website.

iLog Exlixir
Enhance data visualization within Flex and AIR applications with IBM ILOG Elixir.


Creates charts such as bar charts, line charts, pie charts, time series charts, candlestick charts, high/low/open/close charts, wind plots, and meter charts. I wish these charts looked better out of the box, because the features and functionality are good, but the visual design really detracts from the graphs. JFreeChart guys- email me- together we can make the world of JFreeChart a prettier place.

JQuery Plugins

The PHP graphing scripts provide a very easy way to embed dynamically generated graphs and charts into PHP applications and HTML web pages.


JS Charts is a JavaScript chart generator that requires little or no coding. JS Charts allows you to easily create charts in different templates like bar charts, pie charts or simple line graphs.

Kap IT Labs Diagrammer and Visualizer
Kap Lab's Diagrammer provides ready-to-use yet highly customizable multi-layout data visualization and diagramming for Adobe Flex and Air.

Visualizer displays data as graphs to better visualize connections. Kap Lab's Visualizer provides ready-to-use yet highly customizable multi-layout data visualization for Adobe Flex and Air.


A simple to use, yet robust library for transforming table data into a chart. This library uses the HTML5 tag and is only supported on browsers other than IE until ExCanvas gets proper text support.

Open Flash Charts
Open source Flash charts.


PlotKit is a Chart and Graph Plotting Library for Javascript. It has support for HTML Canvas and also SVG via Adobe SVG Viewer and native browser support.


Protovis composes custom views of data with simple marks such as bars and dots. Unlike low-level graphics libraries that quickly become tedious for visualization, Protovis defines marks through dynamic properties that encode data, allowing inheritance, scales and layouts to simplify construction.


Microsoft Silverlight comes with the bar, line, pie, column, and scatter charts.

Telerik Charts for Silverlight, WFP, ASP.NET
Telerik Charts offers rich functionality and data presentation capabilities.

Visifire is a set of open source data visualization controls - powered by Microsoft® Silverlight™ & WPF.

yFiles for Ajax , .NET or Flex
The yFiles product family means state-of-the-art software components for the visualization of networks and diagrams. Unequaled automatic diagram layout, cutting edge graph analysis, and extraordinary visualization.

A few more resources:

Gephi, the open graph Viz platform

XML/SWF Charts is a simple, yet powerful tool to create attractive charts and graphs from XML data.

Bime, Browser-based business intelligence solution (based on Flex)

75+ tools to visualize your data

Kquery-based Highcharts

Flare is an ActionScript library for creating visualizations that run in the Adobe Flash Player

Microsoft Chart Controls, ASP.NET and Windows Forms Chart Controls for .NET Framework 3.5 SP1

Periodic table of visualization methods (data, information,concept, strategy, metaphor)

Popular and Creative
visualization methods

jqPlot Charts and Graphs for jQuery

jQuery Sparklines

AnyChart Flash Chart Component

Chart FX from Software FX has lots of great products for every platform.

Also check out MIT's SIMILE project

Google Vizualisation API with maps and magic-tables

InstantAtlas™ enables information analysts and researchers to create highly-interactive online reporting solutions that combine statistics and map data to improve data visualization, enhance communication, and engage people in more informed decision making.

Dygraph is an open source JavaScript library that produces interactive, zoomable charts of time series. It is designed to display dense data sets and enable users to explore and interpret them.

Mindsetgeometrics allows to build custom charts using predefined SVG files or Adobe Catalyst models.

Seer is a lightweight, semantically rich Ruby on Rails wrapper that provides a seamless interface for the Google Visualization API . It allows to easily create a visualization of data in a variety of formats with a single line of code.

YUI Charts from Yahoo

Silverlight Pivot

AmCharts is a set of Flash charts for your websites and Web-based products. AmCharts can extract data from simple CSV or XML files, or they can read dynamic data generated with PHP, .NET, Java, Ruby on Rails, Perl, ColdFusion, and many other programming languages.

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Thursday, December 17, 2009

The deadly kiss - on allergens and other things you do not want in your system

Be careful who you kiss, especially if you have sensitivities to food, chemicals or other substances you do not want to have in your body.

Richard Gasquet was cleared of doping today, on the grounds that cocaine had been passed into his system from a nightclub kiss.

What else could we get from an innocent kiss?

Remember the tragic story of a peanut allergic teenager from Quebec? Christina Desforges went into anaphylactic shock and died after being kissed by her boyfriend who had just eaten a peanut butter sandwich. An almost immediately administered adrenaline shot didn’t help.

Though not widely recognized, food hypersensitivity by inhalation can cause a lot of problems. 8 top allergens (TEMPS WFS: Tree nuts, Eggs, Milk, Peanuts, Shellfish (crab, lobster, shrimp), Fish (bass, cod, flounder), Wheat, Soy) cause 90% of food allergies. Food related allergies have been on the rise in recent years. Whether this is due to the use of baby creams and lotions (e.g., with a peanut oil content) in early childhood, 20th century hygiene, synthetic & fortified foods or other issues of Western civilization, we need to be careful and think about all possible ways of being exposed.

Epstein-Barr virus (EBV) (causing mononucleosis - infamously known as the kissing disease), Herpes Simplex Virus-1 (causing cold sores) bacterium Streptococcus (causing various infections such as gum disease and strep throat), H.pylori, Candida or other yeast species, Hepatitis B Virus and cytomegalovirus (CMV) are spread via oral transmission from microbe-containing saliva. Many sexually-transmitted diseases follow this route too.

Even cigarettes - besides their harmful toxic chemicals - host a bacterial bonanza —hundreds of different germs, including those responsible for many human illnesses, according to a new study. For example, Campylobacter, which can cause food poisoning and Guillain-Barre Syndrome; Clostridium, which causes food poisoning and pneumonias; Corynebacterium, also associated with pneumonias and other diseases; E. coli; Klebsiella, Pseudomonas aeruginosa and Stenotrophomonas maltophilia, all of which are associated not only with pneumonia but also with urinary tract infections; and a number of Staphylococcus species that underlie the most common and serious hospital-associated infections.

One of the best natural defenses in our saliva is the “good” bacteria and supporting it molecular environment that protects us from settlements of pathogenic microbes and prevents their growth. Some people are more susceptible than others, but everybody should be careful... about whom they kiss.

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Sunday, December 13, 2009

Understanding Your Lab Values: Creatinine test

12th March: KidneysImage by scribbletaylor via Flickr

According to a recent study, reported at the annual meeting of American Society of Nephrology in San Diego. primary care physicians are failing to diagnose chronic kidney disease, especially in women.

Study leader Dr. Maya Rao of Columbia University in New York says primary care doctors typically order a blood test called creatinine to measure kidney function, but this alone is not a particularly accurate measure of kidney function.

Glomerular filtration rate (GFR) is the best test to measure your level of kidney function and determine your stage of kidney disease.
You can calculate your Glomerular Filtration Rate (GFR), by entering results of your blood creatinine test, your age, race, gender and other factors.

The distribution of creatinine test results in 6434 people is shown on the right (NHANES 2006 study, weighted for USA demographics, graph by WolframAlpha)

The typical reference ranges in adult males are 0.7 to 1.2 mg/dL according to Wikipedia and 0.6 to 1.2 milligrams (mg) per deciliter (dl) according to medicinenet. In adult females, it's 0.5 to 1.1 milligrams per deciliter (wikipedia) or 0.5 to 1.1 mg/dl (medicinenet). LabCorps lists normal values between 0.57 and 1.00 mg/dL. (see also reference values for other medical tests and Aurametrix blog on liver tests). Men tend to have higher levels of creatinine because they generally have more skeletal muscle mass than women. Muscular young or middle-aged adults may have more creatinine in their blood than the norm for the general population. Vegetarians have been shown to have lower creatinine levels. Creatinine tends to be slightly lower in pregnancy. It increases with height and body weight. While a baseline serum creatinine of 2.0 mg/dL (150 μmol/l) may indicate normal kidney function in a male body builder, a serum creatinine of 0.7 mg/dL (60 μmol/l) can indicate significant renal disease in a frail old woman.

Infants have normal levels of about 0.2 or more, depending on their muscle development. In people with malnutrition, severe weight loss, and long standing illnesses the muscle mass tends to diminish over time and, therefore, their creatinine level may be lower than expected for their age.

A person with only one kidney may have a normal level of about 1.8 or 1.9. Creatinine levels that reach 2.0 or more in babies and 10.0 or more in adults may indicate severe kidney impairment and the need for a dialysis machine to remove wastes from the blood.

In the United States, creatinine is typically reported in mg/dL, while in Canada and Europe μmol/litre may be used. 1 mg/dL of creatinine is 88.4 μmol/l.

Aurametrix is developing decision support systems to help you evaluate personal health risks, decide on preventative measures, estimate cost/benefits of performing diagnostic tests. Better tools for a healthier world.

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Saturday, December 12, 2009

Vinegar and Water Diet

A glass bottle of commercially produced raisin...Image via Wikipedia

Vinegar and Water Diet was made popular in 1820 by Lord Byron - so says the Fad Diet Timeline (Fad Diets Throughout the Years) article by the American Dietetic Association.

Some people found this diet can do miracles, while others had side effects without any positive results and called it a scam.

The primary reason that this diet works could be that you are told to eat moderate portions, watch the nutritional composition of the food you eat, and get exercise. Just doing those alone is often enough to stimulate your body to maintain a healthy weight, if not lose weight.

Yet, there could be properties in the vinegar that will help you lose weight.

One of the premises of the Apple Cider Vinegar Diet is that taking small amounts of apple cider vinegar daily suppresses appetite and assists in weight loss. Apple Cider Vinegar is also said to reduce glucose levels, treat acid reflux disease and cure acne, among other things. There also were ungrounded claims of cider vinegar to be a special source of various B vitamins and amino acids.

There have been clinical studies, on both rats and humans, suggest apple cider vinegar does make one feel fuller. Many people agree about apple cider vinegar’s ability to suppress appetite (at least because of the taste), but more research is needed. Various other claims of benefits are not supported by research but there is some support for apple cider vinegar’s role in lowering glucose and cholesterol levels and increasing HDL (good) cholesterolin people. Apple cider vinegar was shown to reduce serum triglyceride (TG) levels and increased HDL-cholesterol in diabetic animals.

Another interesting fact is that vinegar was shown to reduce counts of not-so-benefitial bacteria. Diluted solutions of various household sanitizers (apple cider vinegar, white vinegar, bleach, and a reconstituted lemon juice product) were tested for their effectiveness in reducing counts of inoculated Escherichia coli and naturally present aerobic, mesophilic bacteria on lettuce. (J Food Prot 2002,Oct,01;65(10):1646-50; (PMID: 12380754)) Of the sanitizers tested, 35% white vinegar (1.9% acetic acid) was the most effective in reducing E. coli levels (with a 5-log10 reduction after 5 min with agitation and after 10 min without agitation) and in reducing aerobic plate counts (with a >2-log10 reduction after 10 min with agitation).

Could apple cider vinegar be replaced with anything else to achieve the same effects?

Most dieters would answer no to this question. They would tell you to "be careful with which vinegar you use. White vinegar is good for many many thing, but don't drink it will remove all of the minerals and nutrients from your boby. Apple cider vinegar is the only one you want to ingest".

I may say this statement is rather too strong, but what about the actual chemical content?

Comparison of various vinegars shows that no chemical in particularly stands out - apple cider vinegar has a higher Manganese content, but that's about it.

Typical white distilled vinegar is at least 4% acidity and not more than 7%. Cider and wine vinegars are typically slightly more acidic with approximately 5-6% acidity.

Of course, there also could be a yeast and bacterial content - at least dead Acetic acid bacteria (these critters derive their energy from the oxidation of ethanol to acetic acid during respiration. They are Gram-negative, aerobic, and rod-shaped).
Commercially available vinegars, however, are well filtered (no mother of vinegar) and were reported to work in people's diets even if not organic and expensive types.

Usual apple cider vinegar substitutes are:

malt vinegar OR white vinegar (a good choice for pickles) OR wine vinegar (not for pickles)

lemon juice (as a flavoring or for acidulating water) OR lime juice (as a flavoring or for acidulating water) OR brandy (for deglazing pans) OR fortified wine (for deglazing pans and perking up sauces) OR wine (for deglazing pans and perking up sauces) OR ascorbic acid (mixed with water) OR amchoor OR tamarind paste

Since vinegar can be made from anything with sugar, there are probably too many different types to count made in countries throughout the world. Each country may use starting materials native to their area and tailored to the specific tastes of the region.

Typical retail varieties of vinegar include white distilled, cider, wine (white and red), rice, balsamic, malt and sugar cane. Other, more specialized types include banana, pineapple, raspberry, flavored and seasoned (e.g., garlic, tarragon).
Are there Formal Standards for Vinegar?
The following varieties of vinegar are classified by a U.S. Food and Drug Administration (FDA) Compliance Policy Guide for labeling purposes according to their starting material and method of manufacturing:

•Cider vinegar or Apple vinegar is made from the two-fold fermentation of the juices of apples. Vinegar can be made from other fruits such as peaches and berries with the labels describing starting materials.

•Wine vinegar or Grape vinegar is made from the two-fold fermentation of the juice of grapes.

•Malt vinegar, made by the two-fold fermentation of barley malt or other cereals where starch has been converted to maltose.

•Sugar vinegar, made by the two-fold fermentation of solutions of sugar syrup or molasses.

•Spirit or distilled vinegar, made by the acetic fermentation of dilute distilled alcohol.

•Blended Vinegar made from a mixture of Spirit vinegar and Cider vinegar is considered a combination of the products that should be labeled with the product names in the order of predominance. It is also the product made by the two-fold fermentation of a mixture of alcohol and cider stock.

•Rice or Rice Wine vinegar (although not part of FDA’s Compliance Policy Guide) has increased in popularity over the past several years and is made by the two-fold fermentation of sugars from rice or a concentrate of rice without distillation. Seasoned rice or rice wine vinegars are made from rice with the “seasoning” ingredients noted on the label.

•Balsamic vinegar (also not a part of FDA’s Compliance Policy Guide) continues to grow in market share and “traditional” and “commercial” forms are available. The products are made from the juice of grapes, and some juice is subjected to an alcoholic and subsequent acetic fermentation and some to concentration or heating. See the “Today’s Vinegar” section of the Web site for more information regarding Traditional and Commercial Balsamic Vinegar.

Aurametrix is developing decision support systems to help you manage your tests. Better tools for a healthier world.

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