BioMed Search

BioMed Search has been created by Alex Ksikes, a PhD student in University of Cambridge. The goal of BioMed search is to organize figures, images or schema found in biomedical articles. Over 1 Million images have been indexed and more is on its way. BioMed Seach indexes image captions along with the citations to these images.

A sample search with the keyword insulin returns the following result

Insulin resistance is mediated by a proteolytic fragment of the insulin receptor." title="Click to enlarge">

Figure 2: Insulin-induced lipogenesis, glycogen synthesis, and glucose uptake in basal and insulin-resistant 3T3-L1 adipocytes: effects of E64 on insulin resistance. Panel A, effect of E64 on insulin-induced lipogenesis in cells chronically pretreated with insulin. 3T3-L1 adipocytes were pretreated with 1.7 µM insulin alone for 0 (C), 9 (9I), or 18 h (18I) ...

From Insulin resistance is mediated by a proteolytic fragment of the insulin receptor.
The Journal of biological chemistry.

Knutson VP, Donnelly PV, Balba Y, Lopez-Reyes M · 1995 Oct 20

It is the well formated scientific literatures that makes the such search possible. Pay attention and try to improve it.

BioMed Search

BioMed Search has been created by Alex Ksikes, a PhD student in University of Cambridge. The goal of BioMed search is to organize figures, images or schema found in biomedical articles. Over 1 Million images have been indexed and more is on its way. BioMed Seach indexes image captions along with the citations to these images.

A sample search with the keyword insulin returns the following result

Insulin resistance is mediated by a proteolytic fragment of the insulin receptor.

Figure 2: Insulin-induced lipogenesis, glycogen synthesis, and glucose uptake in basal and insulin-resistant 3T3-L1 adipocytes: effects of E64 on insulin resistance. Panel A, effect of E64 on insulin-induced lipogenesis in cells chronically pretreated with insulin. 3T3-L1 adipocytes were pretreated with 1.7 µM insulin alone for 0 (C), 9 (9I), or 18 h (18I) ...

The Journal of biological chemistry.

Knutson VP, Donnelly PV, Balba Y, Lopez-Reyes M · 1995 Oct 20

It is the well formated scientific literatures that makes the such search possible. Pay attention and try to improve it.

My Brain

I participated in a fMRI experiment. Here is my brain.

MY BRAIN

Thanks for Wu Xiang@Cognitive Neuroscience Labratory of USTC













I am amazed to see my brain. Following a silent noise background, my brain appears as a light dot. It become larger and larger, like an approaching distant UFO. Next, my cortex come into sight, however, at first, it looks like an embyro in uterus. It is unset. ( I forgot what I am thinking then). At last, it comes into shape, and shrink, and disappear in the deep noise background again.

Working with Emacs Muse

I have been trying to use emacs muse for the whole afternoon, bacause the frequent breakdown of Google Pages really annoyed me and its low efficiency is unbearable.

I know it is time for me to leave those unstable WYSIYG applications aside and find a stabel and fast solution to maintain my personal homepage. The simplicity and grace of EmacsWiki once catched my eye. After steps of googling, I learned that Emacs Muse has substitute Emacs Wiki as its decendent. Emacs muse is rather easy and enable the full features of Emacs, and it can also output pdf format, maybe I can use it to write reports in the future.

Some Notes:

1. the defaut key for footnote is rather long, it is better to reset it use global-set-key
2. The CSS templates of EmacsWiki can be used for Muse with less changes. Here is a article about the use of Muse

NIC Disabled

Several weeks ago, I encountered a strange problem with a computer, it can start normally, but all network services, such as http, telnet, ping, broke down. After many effort, I gave up and thought some new virus invaded the computer, and suggested to re-install windows. Today, that guy comes, and I asked how about his computer, he explained that the NIC is disabled by the Network Center, possible because his computer with virus automatically spread that virus. OK, NIC disabled, here are some information about it:

How to check if your Network Card is Enabled or Disabled

For Win2000/XP

Right Click on My Computer

Select Properties

Select the Hardware Tab

Click on the Device Manager button and double click on Network Adapters

The Red Cross shows means the Network Card is Disabled.

The one with no Cross means the Network card is enabled.

How To Enable the Disabled Card ?

Right Click on the network card that is disabled and and Click on Enable

Does Indetificatin of Transcriptional Network Take Alternative Splicing Into Accout?

It is boring and tiring to apply for graduate school. However, you will often has the pleasure to find a stranger with the interesting ideas. Two days ago, I noticed a message from a UIUC professor seeking for post-doc students, I visit his lab website. I am attracted by the project of Identification of transcriptional network in his lab, because it focuses on high eukaryote ( more complicated and exciting than YEAST). Alternative splicing flashes in my mind. I wrote his a letter, "It is reported that many high eukaryote's pre-mRNA is subjected to alternative splicing, yielding products of different functions. (it is estimated 40%-50% human genes have the alternative splicing phenomena ) And it proved important in development, such as sex determination. I would like to know whether your research take this post-transcriptional regulation into account. If yes, how do you determine the alternative-splicing sites, via some database or prediction algorithm?" He replied soon, but don't touch this topic. Any ideas?

Why Europeanian discovered theory of continental drift?

Why it is European, Alfred Wegener, who discovered the theory of continental drift? I guess it can be explained by the different world maps an European, an Asian, and an American will see.

Europeans sees












Asian sees











Finally, an American finds the world is like this

Systems Biology Review Series

Nature release recently a series of reviews on systems biology. I have long been hoping to read these papers, however cannot help becoming lazy in leisure senior grades.

Today my eye is caught by the opening line of Collecting and organizing systematic sets of protein data. It states, "The goals of systems biology are orthogonal to large-scale efforts to catalogue genomes, proteomes and interactomes.". I found it a novel expression because I nearly be used to the tone of "omics", and I have a strong feeling that there is always a new idea behind a novel expression. I continue with the paper.

Following the striking opening line comes a sound argument: organism is heterogenous and biological process is dynamic; thus, systems biology require dynamic, spatially resolved data on gene and protein function; This type of data is complex, thus data must be collected with reference to specific, quantitative models.

The authors say practical trade-offs must be considered when selecting what to measure and how frequently to measure it. I wonder whether we can build a model to model the experimental process instead of a preliminary experiment, or at least the experiment model give some insight into the process before the indispensable preliminary experiment.

About the third point data fusion, no single method is sufficient to measure the full diversity of protein signals. On the other hand, even there really exist a general method, how can we believe it gives the right data, given the inaccuracy of biological experiment. Therefore, data fusion also means error detection.

About mass spectrometry, the biggest limitation is not the instrumentation, but rather inadequate software and the need to confirm peptide assignments by hand. Further reading needed to confirm whether it is a rich land.

Computed metrics: In the paper analysis of cellular biology, I made a analog that the change of magnetic field incites electronic field, we biologist have long focus on the absolute level of protein or gene, but the change may make difference, however we have no a method to characterize the change until now. The section express similar idea.

Alterbative Splicing--Christopher Lee, Jacek Majewski

Profossor C. Lee and professor J. Majewski conduct research in alterbative splicing using bioinformatics method.

Professor Lee : http://www.uclaaccess.ucla.edu/UCLAACCESS/Web/Faculty.aspx?ri=434
Professor J. Majewski: http://genomequebec.mcgill.ca/majewski/

Need a review of their method and focus.
Professor Black, Doug also engage research in alternative splicing, from a more traditional chemical and biological perspective

Bioinformatics -- Andy Baxevanis Ouellette BFF

Baxevanis, A.D and Ouellette B.F.F coauthored a book Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins. This book is updated to the 3rd edition in 2005.

Baxevanis's previous work focus on computation analyis of disease-causing mutations from a structural standpoint, using innovative approaches to deduce the prisece structure change in protein cause by a specific genetic mutation. (What method?)

During the early development of microarray, Baxevanis's group developed the first publicly available program to restore and analyze microarray data.

Now, Baxevanis's group the group developed a software program known as GeneLink, which enables researchers to analyze large data sets from studies of complex-trait genetic disorders, such as cancer, diabetes, and hypertension, which involve many genes along with environmental factors.

Quelette is the head of UBC Bioinformatics Centre (UBiC) and this graduate program is worth of time to have a look.

Bioinformatics -- Philip E. Bourne , Helge Weissig

This post is about Philip E. Bourne , Helge Weissig, two pioneer in structural bioinformatics. They coauthored a book Structural Bioinformatics. P.E.Bourne sumerize his lab's goal as follows in UCSD.

"Our goal is to undertake in silico bioinformatics-related research and education. Along the way we develop resources, for example, the RCSB Protein Data Bank(PDB) and the Immune Epitope Database (IEDB), for use by the community. We view these resources as being as important as disseminating our science through the scientific literature. We firmly support open access to the scientific literature through our work with the Public Library of Science and free access to our software"

P.E.Burne's group develop and maintain several databases

Biological Structure
The Protein Data Bank (PDB)	The single worldwide source of primary structural data on biological macromolecules determined experimentally. Developed in collaboration with Rutgers University our partner in the Research Collaboratory for Structural Bioinformatics (RCSB).
Domain Assignment (PDomains)	The main goal of this resource is to better understand principles behind structural domains identified from 3D coordinates ref .
Structure Comparison Database (CE)	Pair-wise structure comparisons based on the Combinatorial Extension (CE).
Common Subdomains	Compilation of recurring protein substructures.
Extended GO Annotation of PDB Chains	Use of structure comparison to extend the coverage of GO terms in the PDB.
Protein DNA Complexes	Automated classification of protein-DNA complexes of known structure.
Multiple Structure Alignment CE-MC	Starting from CE pair wise alignments a multi-structure alignment is computed using a Monte Carlo optimization technique.
Signal Transduction
The Protein Kinase Resource (PKR)	A compilation of structures, structure alignments, sequences and sequence alignments for the protein kinase family.
Apoptosis
Apoptosts-DB	Known domains involved in apoptosis and associated sequence alignments.
Immunology
Immune Epitope Database (IEDB)	Information that facilitates the dissemination of immune epitope information, the generation of new research tools, diagnostic techniques, vaccines and therapeutics for emerging and re-emerging diseases.

Helge Weissig's work centers around the research and education in strutural bioinformatics. His personal wedsite provide good directions on resoures in this field and a serise introductory courses
http://www.bioinformaticscourses.com/

Bioinformatics -- Sean Eddy

Sean Eddy's most significant contribution is that he suggests and developed many tools based on probabilistic models of biological sequence and structure. Hidden Markov models (stochastic regular grammars) are useful for primary structure analysis of proteins and DNA. Stochastic context-free grammars are ideal for analysis of RNA secondary structure.

His work include include the HMMER profile HMM search software and the Pfam protein domain database; the Infernal structural profile SCFG search software for RNAs and the Rfam RNA domain database; and the QRNA genefinding program for ncRNA genes.

He also apply probabilistic modeling and other computational algorithms to identify interesting genetic features in large-scale DNA sequence.

His work in this area is summerized his book

Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
by Richard Durbin, Sean R. Eddy, Anders Krogh, Graeme Mitchison


Now, he focus on identifying novel structural and catalytic RNAs. He proposed the "modern RNA hypothesis" stating that: far from being a few scattered relics, RNAs are in fact in widespread use in modern organisms in a variety of roles. We now argue for a “modern RNA world” hypothesis: many of the RNAs we see today are modern inventions, highly adapted to regulatory roles in complex organisms.

Quotations: Microarray: Quality Control

Today I read a paper Microarray: Quality Control in Nature , and copy some quotations of masters in these field. Funny? Maybe, we need a master to lead the way.

The challenge is no longer how to generate these vast bodies of genomic data, but rather in how to best collect, manage, and analyze the data.

by John Quackenbush

Changing these algorithms (used to convert spot flurescence to gene-expression estimates.) can make a difference, and you can turn an experiement that looks just so-so into something that looks powerful and precise.

by Rafael S. Irizarry

We are facing too many options for analyzing the same data set, and there has not been adequate scientific vetting of the capabilities and and limitations of available methods.

by Leming Shi

High-quality samples and high-tech instrumentation alone won't save the microarray experiment. Some of the most fundamental challenges lie in gleaning biological signicance from mounds of data and designing experiments with a statistically sound foundation

by Michael Eisenstein

I am playing gample

These days I have been spending hours surfing the websites of Graduate school in order to find a right school in the meaning that I will be proud of entering it and it will be satisfactory of accepting me. There are so many schools and so many mentors that I can not make a choice. I am just playing a gamble.

When I decided to enter an university three years ago, I didn't have such a tough time because my family helped me and the universities are in China. But this time, I am going to study in America which I have never been and is unfamiliar with. It is said America has many good schools and more opportunities. Like the people on the boat of Mayflower, I cherish this dream and take the risk to pursue it.

This morning, my roommates, who is also preparing to study overseas, told me he dreamed that I reveived many offers last night. I hope it is a good signal to me.

When gmail disabled

Were your gmail disabled? I noticed a discusion about this problem. If you have any browser extensions, toolbars, or third party software intended to interact with Gmail, especially when such software involves too much data transfer, Google may decide to disable your gmail account, some temporaliry, some for ever. Goole list some example, such as GmailFS, Greasemonkey. I myself understand the justice of google's actions, and believe that google won't betray its don't be evil motto, thought I noticed greasemonkey, one of my favourite firefox extensions, is on google's blacklist .

If your gmail is unfortunately banned by google,there is a site to complain https://mail.google.com/support/bin/request.py?lockout=1

[From Google Reader] Related articles in Google Scholar

Related articles in Google Scholar

Google Scholar recently added the ability to find related articles for a paper. Its is a link Related Article together with cited by and webseach attched to each search result. if not notified by offical google blog post, I would have neglected it. Some one tried it, and writes:

"so I decided to try it out with a paper from my former life as a graphics person. It was a paper in SIGGRAPH a few years ago called the "Office of the Future" and it dealt with projecting images onto surfaces that aren't exactly flat. If you predistort an image before you project it, you can often cancel out the different surfaces as you project onto them, which lets you create the appearance of a flat screen again. Here's a picture that gives you the idea. It's completely unrelated to me or the paper, but it demonstrates the concept really well (I just did a flickr search for [projection surface] and found a nice result–thanks flickr! I don't read German,... Source: http://www.mattcutts.com/blog/related-articles-in-google-scholar/ "

Matlab-SP3

Matlab 7 With Sp3

Matlab 7 With Sp3 (full 3 Cd ISO)

MATLAB is a high-level technical computing language and interactive environment for algorithm development, data visualization, data analysis, and numeric computation. Using MATLAB, you can solve technical computing problems faster than with traditional programming languages, such as C, C++, and Fortran.

You can use MATLAB in a wide range of applications, including signal and image processing, communications, control design, test and measurement, financial modeling and analysis, and computational biology. Add-on toolboxes (collections of special-purpose MATLAB functions, available separately) extend the MATLAB environment to solve particular classes of problems in these application areas.

MATLAB provides a number of features for documenting and sharing your work. You can integrate your MATLAB code with other languages and applications, and distribute your MATLAB algorithms and applications.

Key Features:
High-level language for technical computing
Development environment for managing code, files, and data
Interactive tools for iterative exploration, design, and problem solving
Mathematical functions for linear algebra, statistics, Fourier analysis, filtering, optimization, and numerical integration
2-D and 3-D graphics functions for visualizing data
Tools for building custom graphical user interfaces
Functions for integrating MATLAB based algorithms with external applications and languages, such as C, C++, Fortran, Java, COM, and Microsoft Excel

31 parts x 50 MB


Download links in coments.

1 Comments:

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Why my blog is called warm sping harbor lab

I invent the term Warm Spring Harbor Lab myself with the inspiration of the famous Cold Spring Harbor Lab, a international biological science research institute which sees the revolution of molecular biology. WSHL is a kind joke of CSHL. Another source is that the Anhui province, in which my university locates, actually have many warm springs in the Huangshan Mountain region. The third consideration is that I am always thinking of this term. I hope to set up such a institute in China, and promote the development of science in my country.

I used to think I am the first one to invent this term. However, I google it just now and found a papers in Science magazine published in 2004 had touched this name. Unfortunately, I fall behind.

Avril Lavigne

This is the first time I listen to Avril Lavigne. Long before today I have noticed her beautiful name and grace posters. She rarely smiles. She impress you with a remote and pride attitude, something like a girl in one of Murakami Haruki's novel, Dance! Dance!Dance! this kind of girls have a talent to observe and control others. however, I didn't become a fan of Avril then because I have seen too many quick-coming-and -quick-going singers with a beautifle face but an ugly voice. I have a prejudice toward newly emerging actrees.

My idea changed when I come to losing grip, the first song of the album Complicated. Her style is a little like Sun Yanzi, relaxed and comfortable. I continued. the song complicated convert me to a funs of Avril. And then,Tomorrow. The voice souds so sweet that I feel my sweetheart whisp around my ears.

I have just listen to Avril, I can only recommend the following

• complicated
• skater boy
• tomorrow

List to be continued.

 

Avoiding RSI

Avoiding RSI: "Posted by Dr. Taraneh Razavi, M.D., Staff Doctor

From time to time, a resident physician at Google headquarters weighs in with her thoughts on healthy living. This is not medical advice, and you should check with your own doctor before pursuing any particular course of action.

There is a Chinese saying that 'To go beyond is as wrong as to fall short.' In other words, how long can you tap on that keyboard or sit in that chair before you hurt yourself. We’re not designed to remain as sedentary or perform the fine motor movements for the long uninterrupted hours that we have to do in so many of our jobs. Evidence suggests that prolonged abnormal posture and repetitive movements contribute to neck, limb and back pain. These conditions are collectively known as overuse syndromes, or repetitive stress injury (RSI).

RSI is no small matter. It accounts for 34% of all lost-workday injury and illness — and costs almost $20 billion annually, according to the Bureau of Labor Statistics. The National Academy of Sciences has concluded that an estimated $"

This year's Anita Borg Scholarship winners

This year's Anita Borg Scholarship winners: "Posted by April Yu and Jennifer Bostrom, University Programs

It's that time of year when we happily announce the winners of the 2006 Google Anita Borg Memorial Scholarship. We're awarding 19 $10,000 scholarships to these outstanding young women -- graduate and undergraduate students who are completing degrees in computer science and related fields -- with our congratulations:



Brianna Bethel, University of Colorado - Boulder
G. Ayorkor Mills - Tettey, Carnegie Mellon University
Gillian Rachael Hayes, Georgia Institute of Technology
Himabindu Pucha, Purdue University
Karen Fullam, University of Texas at Austin
Kristen Walcott, University of Virginia
Kristina Chodorow, New York University
Laura Rouse, Georgia Institute of Technology
Marta Magdalena Luczynska, Massachusetts Institute of Technology
Megan Olsen, University of Massachusetts Amherst
Michele Banko, University of Washington
Neven Abou Gazala, University of Pittsburgh
Parisa Michelle Tabriz, University of Illinois, Urbana-Champaign
Rebecca Nancy Nesson, Harvard University
Shana Kay Watters, University of Minnesota
Sharmishtaa Sesha"

Who can introduce me to orkut

I wanna sign to orkut at google, who can introduce me to it?