Wait

Sorry,my blog is unreachable in China, faint. It is blocked for some political reasons.

Go,go! BEAT LA!

红屯兵们振臂一呼“打到胡人”的时候到了，Ymao主席万岁。能不能到天使城的机票不要钱啊？

Enrollment Update for the Personal Genome Project‏

"PGP-10" to "PGP-100" & beyond.
Details in my hotmail E-mail box.

Some Chinese companies of gene test

http://www.zdens.com
http://www.adinovo.com/
http://www.qxjyok.com.cn/
http://www.xcmjy.com/
http://www.yigene.com/

Launch Your Career with LinkedIn

http://grads.linkedin.com/

公子说：不周山的倒下

醉卧沙场君莫笑，古来征战几人还？

“对我来说，职业生涯就此终结。”

“这样的结果不属于我的计划，现在我只能说我很开心能打18年的篮球，这18年没有过伤病困扰。我十分感谢上帝能保佑我，能让我的NBA生涯周围一直能有如此多的伟大球员。我只是很开心。”

“我要高昂着我的头颅，不会失望，不会懊悔。在我18年职业生涯中我感谢能有如此多的经历。”

“当我躺在球场上时，我为之流泪。但是当我回到休息室时，Keith Jones(火箭训练师)和我聊天，告诉我要乐观，我要感谢上帝能在18年中给予我如此美好的生活。能有如此美妙的职业生涯我已经无憾，我能在球场上完成那么多伟大的成就，可以对如此多的年轻球员有所影响，能让我自己成为一个模范球员，我已经不能再要求更多。”

祝福伟大的Dikembe Mutombo，老兵永远不会死，他们只会老去。

hoop一天就到了89楼，大叔永远是个传奇了。

Faint!

神棍在第一轮已经被打破，带主观色彩的神棍肯定是不行的。Houston，GO,GO,GO!

Galaxy (http://galaxyproject.org/)

I think this project is very interesting.It focus extensively on design of best practice workflows for biological applications of NGS data including re-sequencing, de novo assembly, metagenomics, transcriptome analysis and epigenetics.
By the way, they are recruiting new intelligence.

To be a Yesmam

Don't say no to anything coz nothing is impossible.Be more active.

心里的山

今天在CCTV看了老兵陈俊贵在天山为战友守陵24年的故事，我和老婆都流泪了。世界上最难攀越的山不在天边，而是在人的心里。

今天三个值得讲的事情，注重细节。

1.跟爸爸聊了电子商务，爸爸说以后让我别小气，他要找我在网上买东西，哈哈。
2.无意中看到钟南山院士的一句话，类似讲生活方式是自己选择的，你可以选择健康的方式。
3.偶尔走到老夏的荒园：壶酒醉花间 荚蝶乱眼帘 风徐灯弄影 月朗水融天。老夏真洒脱，自传都开写了，会玩啊！

其实生活中有很多点滴是多彩的！

忍不住 神棍 一下。

今年NBA排赛程的人太有才了，精彩极了。

最后一轮神棍(客前主后)：
爵士 vs 湖人，几乎百分之百湖人胜，宜将剩勇追穷寇的道理，据说澳门的盘口开到9了，没有任何理由不赢。

黄蜂 vs 马刺：马刺赢，我不相信黄蜂真的是隐藏实力，但马刺必须争主场优势。
火箭 vs 小牛：小牛也想赢，但是不是很迫切？反之火箭非常迫切要主场优势。
掘金 vs 开拓者：开拓者会拼命拿下这场，胜算较大。

最后排名：湖、火、掘、开、刺、蜂、牛、爵

季候赛对阵：

湖对爵；火对牛；掘对蜂；开对刺；

二轮预测：

湖对刺；火对掘；

西部决赛预测：

湖对火；

总决赛预测：

湖对骑；

总冠军预测：

湖人。

到时候谜底揭开时看神棍程度，全对则需奖。

重温了一下一部让我感动的电影

从而家开始,你净系锡我一个,要纵我,唔准呃我,应承我嘅每一件事都要做到,每一句话都要真心,唔准虾我闹我,要信我,有人虾我你要等一时间出嚟撑我,我开心你要陪我开心,我唔开心你要氹我开心.永远都要觉得我系最靓嘅,发梦都要见到我,喺你心里面只有我!

从现在开始，我只疼你一个。
我会宠你，决不会骗你。
答应你的每一件事情，我都会做到。
对你讲的每一句话，都是真话。
不欺负你，不骂你，会相信你。
有人欺负你，我会第一时间出来帮你。
你开心的时候，我会陪着你开心；
你不开心，我也会哄得你开心。
永远觉得你最漂亮，做梦都会梦见你。
在我的心里，永远只有你一个。

哈哈，山上的朋友们大家好，你们知道我说的是那部电影了吗？我发现其实我的感情就是那样细腻，我爱我的老婆！

A hint

我接触的领域中发现stanford的学生的创业精神最强，值得学习！Larry就是stanford的哦。
http://www.stimulomics.com/

थ्री job दताबसेस फॉर लाइफ साइंस!

http://www.monster.com/
http://www.biospace.com/
fttp://www.naturejob.com/

Make some transitions for my web surffing.

From DXY, lqqm, mop, sina, hoop, hexun to facebook, nature network, reseacherID, Epernicus, LinedIn, Seqanswer, bioinformatics.org etc.

Makers:
http://www.researcherid.com
http://network.nature.com/
http://www.epernicus.com/

Pay more attention to these blogs

http://scienceblogs.com/geneticfuture/
http://thegenesherpa.blogspot.com/

Very good content for personal genomics.

My newly published papers in 2009

1. Transcription and splicing regulation in human umbilical vein endothelial cells under hypoxic stress conditions by exon array. Hang X, Li P, Li Z, Qu W, Yu Y, Li H, Shen Z, Zheng H, Gao Y, Wu Y, Deng M, Sun Z, Zhang C. BMC Genomics. 2009 Mar 25;10(1):126. PMID: 19320972

2. REMAS: a new regression model to identify alternative splicing events from exon array data. Zheng H, Hang X, Zhu J, Qian M, Qu W, Zhang C, Deng M. BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S18. PMID: 19208117

3. Exon array data analysis and new algorithms for alternative splicing identification. HANG Xing-Yi, DENG Ming-Hua, SUN Zhi-Xian, ZHANG Cheng-Gang. Bulletin of the academy of military medical science. (Chinese) Accepted.

The second paper is based on the cooperation with Peking University and I am one of the co-first authors. I have given an oral presentation of the same topic in APBC (Asia Pacific Bioinformatics Conference) 2009. It is notable that this paper is one of the two papers of Best Paper Awards in APBC2009.

Finally, pray for my ongoing project of stroke disease. Good luck!

Differentiation in bioinformatics

Chase up the trends of new in silico biology.

Read more papers of Plos CB and MSB. Comparing with Bioinformatics and NAR, I find Plos CB and MSB prefer to inspire the new application to functional biology. New computational biology and systems biology blaze the promising way in functinonal biology.However, bioinformatics will never fade aways but play more roles as technological skills.

牛年好兆头，老婆中奖得了个金牛，还周大福的呢！

真的，金牛这年头每个人都太需要了，特别是金融危机下的牛年啊。
上图：

Nature Review Genetics research highlights

Nature Review Genetics volume 10 February 2009

ALTERNATIVE SPLICING: Deciding between the alternatives

"altered splicing patterns might be more important than expression changes in determining complex human traits."

ORIGINAL RESEARCH PAPERS
Yu, Y. et al. Dynamic regulation of alternative splicing by silencers that modulate 5′ splice site competition. Cell 135, 1224–1236 (2008)
Heinzen E. L. et al. Tissue-specific genetic control of splicing: implications for the study of complex traits. PLoS Biol. 6, e1000001 (2008).

GenBlastA: enabling BLAST to identify homologous gene sequences.

Sequence analysis is the central topic of bioinformatics all along.

Genome Res. 2009 Jan;19(1):143-9. Epub 2008 Oct 6.

GenBlastA: enabling BLAST to identify homologous gene sequences.

She R, Chu JS, Wang K, Pei J, Chen N.

School of Computing Science, Simon Fraser University, Burnaby, British Columbia, V5A 1S6 Canada.

BLAST is an extensively used local similarity search tool for identifying homologous sequences. When a gene sequence (either protein sequence or nucleotide sequence) is used as a query to search for homologous sequences in a genome, the search results, represented as a list of high-scoring pairs (HSPs), are fragments of candidate genes rather than full-length candidate genes. Relevant HSPs ("signals"), which represent candidate genes in the target genome sequences, are buried within a report that contains also hundreds to thousands of random HSPs ("noises"). Consequently, BLAST results are often overwhelming and confusing even to experienced users. For effective use of BLAST, a program is needed for extracting relevant HSPs that represent candidate homologous genes from the entire HSP report. To achieve this goal, we have designed a graph-based algorithm, genBlastA, which automatically filters HSPs into well-defined groups, each representing a candidate gene in the target genome. The novelty of genBlastA is an edge length metric that reflects a set of biologically motivated requirements so that each shortest path corresponds to an HSP group representing a homologous gene. We have demonstrated that this novel algorithm is both efficient and accurate for identifying homologous sequences, and that it outperforms existing approaches with similar functionalities.

PMID: 18838612

Url: http://genome.sfu.ca/projects/genBlastA/

笔记

么事不去骨干版，无聊人居多；
么事不看其美贴，低俗者居多；
么事少去新浪网，意淫贴居多。

难事常有，多看多想必有路。凡事不要急，耐心探索必有路。

A potential and new drug for stroke, another one.

Nature Reviews Drug Discovery Volume 8 | March 2009 | 183

The FDA’s Cardiovascular and Renal Drugs Advisory Committee voted in favour of approving prasugrel, an oral anticoagulant developed by Daiichi Sankyo and Eli Lilly.

The advisory committee, however, agreed that the benefit of preventing myocardial infarction, cardiovascular death and stroke outweighs the risk of major bleeding, such as haemorrhages, and voted 9–0 in favour of prasugrel approval.

来自团长和天天的启发

今天看《我的团长我的团》，Mike愤怒且感动地说：“你是我见过的最热爱士兵的军官，因为你什么都没有。” 是的，龙文章除了理想确实什么都没有，为了拥有自己的团，为了打鬼子，他说了无数的谎话，但是都是为了理想。“回家不积极，脑袋有问题”，呵呵！要用最朴素和真诚的言语去打动你的部下。其实作为团长，龙文章的压力和责任是最大的。在片中好几处都不经意的表现出来，作为一个团长既要实现自己的理想，又要对兄弟们的生命负责，对于炮灰团来讲这个压力何其之大。所以当Mike开车扬长而去之际，他执意要步行回去，好好缓解一下吧！他也苦笑着地对Mike讲：“我羡慕你能说这样的话----这不是我职责范围内的事。”

昨天天天也说了同样的话，当你的理想刚起步的时候是经不起折腾的，只有“哄”着你的手下，用你的真心去感化和团结他们。XY也说：“我要和员工一起出去玩的，不能脱离他们”！是这样的。

我今天离开实验室看见师弟、师妹们忙碌的身影，我突然有所感想：无论是谁，当你接近或实现理想的时候，千万不要持有苛求的态度，要有一颗宽容博爱的心，要力求公平。只有强者的社会必定是不稳定的。

Thanks gifts from Harvard B.

Hi, B. I am so appreciated that you bring me so many "treasures" from uncle Sam. Declaration of Independence, Switzerland caillers and especially the "The Last Lecture", which will inspire me to live each day of my lives with purpose and joy.

By the way, I have shared your "caillers" with my lab colleagues, very tasty.

NGS Alignment Programs and comments from Sanger experts

Cite from http://www.sanger.ac.uk/Users/lh3/NGSalign.shtml

Software

Currently, this page only includes software I am familiar with. Most of them aim for aligning next-generation sequencing (NGS) data and were developed since 2007. I may extend the list when I have time. Several notes:

• The programs are listed in the alphabet order in each category.
• Features shown in brackets are optional and may affect efficiency.
• The version number shown for each program is the one I have checked, but may not be the latest.

Indexing Reads with Hash Tables

• Cross_match [1.080730]. The latest cross_match has been substantially improved for short read alignment. Its speed is comparable to other aligners and might be the best choice for local alignment.
  • Platform: Illumina; 454
  • Features: gapped alignment (maximum 2 gaps in the fast mode); local alignment
  • Availability: academic free source codes
• Eland [1.0]. Probably the first short read aligner. Eland substantially influences many aligners in this category and still outperforms many followers. Although it is not the fastest any more, it is close to the fastest and has the smallest memory footprint. Eland itself works for 32bp single-end reads only. Additional Perl scripts in GAPipeline extend its ability.
  • Platform: Illumina
  • Features: PET mapping; mapping quality; SNP caller; counting suboptimal occurrences.
  • Advantages: fast; light-weighted
  • Availability: free source codes for machine buyers.
• MAQ [0.7.1, PMID: 18714091]. This is my program to align short reads and to call variants. It has been used in several high-profile papers.
  • Platform: Illumina; SOLiD (partial)
  • Features: PET mapping; quality aware; gapped alignment for PET; mapping quality; adapter trimming; partial occurrences counting; SNP caller
  • Advantages: feature rich; publication proved
  • Limitation: up to 128bp reads; no gapped alignment for single-end reads
  • Availability: GPL
• RMAP [0.41, PMID: 18307793]. One of the earliest short read aligners.
  • Platform: Illumina
  • Features: quality aware; [gapped alignment]; best unique hits
  • Availability: GPL
• SeqMap [1.0.8, PMID: 18697769]. An Eland-like program.
  • Platform: Illumina
  • Features: [gapped alignment]
  • Limitation: not counting suboptimal hits
  • Availability: GPL
• SHRiMP [1.10]. Q-gram based algorithm.
  • Platform: SOLiD; Illumina; 454
  • Features: SOLiD mapping; gapped alignment; potential support for mapping quality
  • Limitations: a little slow
  • Availability: GPL
• ZOOM [1.2.5, PMID: 18684737]. Eland-like algorithm with the improvement of using spaced seed. ZOOM supports longer reads and faster than Eland, although it uses more memory. ZOOM is feature rich, but some features may come at the cost of speed.
  • Platform: Illumina; SOLiD
  • Features: PET mapping; SOLiD mapping; [gapped alignment]; [mapping quality]; [quality aware]
  • Advantage: fast; feature rich
  • Limitation: up to 224bp reads; gapped alignment comes with cost
  • Availability: commercial

Indexing Genome with Hash Tables

• BFAST [0.3.1] (alternative link).
  • Platform: Illumina; SOLiD
  • Availability: academic free
• MOM [0.1, PMID: 19228804].
  • Platform: Illumina; (?)
  • Features: counting suboptimal occurrences; local alignment
  • Availability: free
• Mosaik [0.9.891]. Although I have not tried personally, Mosaik has been used in several high-profile publications and delivers good performance.
  • Platform: Illumina; 454
  • Advantages: long reads
  • Availability: academic free binary
• NovoAlign [2.0]. NovoAlign competes with MAQ on speed and feature set, and may be more accurate than MAQ. It also implements several features missing in MAQ.
  • Platform: Illumina
  • Features: PET mapping; gapped alignment; mapping quality; quality aware; adapter trimming; MAQ format
  • Advantages: highly accurate; gapped alignment; feature rich
  • Requirements: >8GB RAM for paired-end mapping against the human genome.
  • Availability: proprietary; academic free binary (no multi-threading support)
• PASS [0.5, PMID: 19218350].
  • Platform: Illumina; SOLiD; 454
  • Features: PET mapping
  • Advantages: long reads
  • Requirement: >15GB RAM against human genome
  • Availability: free source codes to academic users
• RazerS [20081029]. Based on the SeqAn library.
  • Availability: free source codes
• SOAPv1 [1.11, PMID: 18227114]. The first published short read aligner.
  • Platform: Illumina
  • Features: PET mapping; adapter trimming; gapped alignment; SNP caller; counting occurrences
  • Advantages: feature rich
  • Requirements: >14GB RAM against human genome
  • Availability: GPL

Merge Sorting

• Slider [0.6, PMID: 18974170]. A very clever short read aligner specifically designed for Illumina reads. It is able to use the second best base call, which potentially improves the accuracy on SNP finding.
  • Platform: Illumina
  • Features: Using second base
  • Advantages: fast; potentially more accurate on SNP discovery
  • Requirements: >160GB disk space
  • Availability: free source codes

Indexing Genome with Suffix Array/BWT

• Bowtie [0.9.9]. This is probably the fastest short read aligner to date. Although under the default option Bowtie does not guarantee to find the best hit or tell if the hit it finds is unique, it is possible to improve this behaviour at the cost of speed.
  • Platform: Illumina
  • Features: partial PET mapping; quality aware; [mapping quality]
  • Advantages: very fast
  • Availability: GPL
• BWA [0.4.5]. Another aligner written by me. Given high-quality reads, it is an order of magnitude faster than MAQ while achieving similar alignment accuracy.
  • Platform: Illumina; SOLiD (in development)
  • Features: PET mapping; gapped alignment; mapping quality; counting suboptimal occurrences; SAM output
  • Advantages: fast
  • Limitations: slow for long reads and reads with high error rate
  • Availability: GPL
• SOAPv2 [2.0.1]. A marvelous program developed by the group who wrote BWT-SW. The current version of SOAPv2 performs best for reads containing no more than 2 mismatches.
  • Platform: Illumina
  • Features: PET mapping; mapping quality; counting occurrences
  • Advantages: fast
  • Availability: academic free binary
• vmatch [SpringerLink].
  • Availability: academic free binary

Recommendation

First of all, as I am the key developer of two short read aligners (BWA and MAQ), it is really hard for me to give an unbiased evaluation. Please bear this fact in mind when reading through my comments below.

For Illumina reads, I would recommend my program BWA. BWA implements most of the major features of a practical aligner. It is relatively small in memory and highly efficient with little tradeoff on accuracy. BWA outputs alignment in the SAM format. Users may use SAMtools to sort/merge alignments and to make variants calls. One potential concern about BWA is it has not been widely used at the moment. It may be less robust than those publication-proved aligners such as Eland and MAQ.

Mapping inconsistent read pairs with NovoAlign is recommended for PET-based structural varition detection where alignment accuracy is the leading factor on reducing false positive calls. NovoAlign is the most accurate aligner to date.

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Affymetrix and Genisphere Launch Best-in-Class Solution for microRNA Expression Research

Benefits include fastest labeling assay on the market and industry-leading array content covering 71 organisms.

http://www.affymetrix.com/products_services/arrays/specific/mi_rna.affx

Con for my paper!

Editorially accepted manuscripts: Transcription and splicing regulation in human umbilical vein endothelial cells under hypoxic stress conditions by exon array
BMC Genomics

Bookmarker of "Fundamentals of Biostatistics"

1-30.

I think the editors fo Bioinformatics are angry.

They are angry about the messy situation of submissions on microarray analysis. An explicit requirement for these topics has been ruled. Please pay attention to the editorial before you submit similar papers to Bioinformatics.

See http://bioinformatics.oxfordjournals.org/cgi/reprint/25/6/701.

Breaking news today

NIH gets slight boost in 2009 budget
Washington, DC, Mar. 11—President Obama has signed a spending bill that includes a slight increase in funding for the National Institutes of Health for fiscal year 2009, which began Oct. 1, 2008. The NIH 2009 budget is $30.3 billion, a 3.2% increase from last year.

I just wonder if the budget increase is enough to offset expected inflation?

Obama lifts embryonic stem cell research ban
Washington, DC, Mar. 9—U.S. President Barack Obama signed an executive order that lifted the ban on federal funding for embryonic stem cell research.

From Biotechniques.

Sequencing literature watch

1. Finding the fifth base: Genome-wide sequencing of cytosine methylation.
Lister R, Ecker JR.
Genome Res. 2009 Mar 9. [Epub ahead of print]
PMID: 19273618

2. Massively parallel sequencing of the polyadenylated transcriptome of C. elegans.
Hillier LW, Reinke V, Green P, Hirst M, Marra MA, Waterston RH.
Genome Res. 2009 Mar 6. [Epub ahead of print]
PMID: 19181841

Molecular Cell, Volume 33, Issue 5, 547-558, 13 March 2009
Article
Single-Stranded DNA Orchestrates an ATM-to-ATR Switch at DNA Breaks
Bunsyo Shiotani1andLee Zou1,2,Go To Corresponding Author,
1 Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA 2 Department of Pathology, Harvard Medical School, Boston, MA 02115, USA


Summary

ATM and ATR are two master checkpoint kinases activated by double-stranded DNA breaks (DSBs). ATM is critical for the initial response and the subsequent ATR activation. Here we show that ATR activation is coupled with loss of ATM activation, an unexpected ATM-to-ATR switch during the biphasic DSB response. ATM is activated by DSBs with blunt ends or short single-stranded overhangs (SSOs). Surprisingly, the activation of ATM in the presence of SSOs, like that of ATR, relies on single- and double-stranded DNA junctions. In a length-dependent manner, SSOs attenuate ATM activation and potentiate ATR activation through a swap of DNA-damage sensors. Progressive resection of DSBs directly promotes the ATM-to-ATR switch invitro. In cells, the ATM-to-ATR switch is driven by both ATM and the nucleases participating in DSB resection. Thus, single-stranded DNA orchestrates ATM and ATR to function in an orderly and reciprocal manner in two distinct phases of DSB response.

A good search engin for PubMed using computational linguistics methods

http://www.semedico.org/

High-Performance Gene Name Normalization with GENO.
Wermter J, Tomanek K, Hahn U.
Bioinformatics. 2009 Feb 2. [Epub ahead of print]
PMID: 19188193
http://bioinformatics.oxfordjournals.org/cgi/content/full/25/6/815

Today's Nature Technology Feature: The digital generation:

NATURE|Vol 458|12 March 2009
Next-generation sequencing is pushing gene-expression profiling further into the digital age. But analog methods still have plenty of wind left. Nathan Blow looks at the looming battle over the cell’s transcriptome.

一场没有硝烟的战争？蜃景中的交锋？It's my time.

Products:
SOLiD™ System Sequencing Whole Transcriptome Analysis
Illumina Genome Analyzer Applications Transcriptome Analysis
1.mRNA-seq
2.tag profiling
3.small RNA discovery and analysis
Roche 454 Life Science SAGE based expression profiling on GS FLX system

“For digital gene expression you are just counting the number of times you hit a gene and then assuming that that represents the number of copies of the transcript that you have in your population,” says Chad Nusbaum.

In addition to looking at RNA expression patterns, RNA-seq can allow researchers to discover new classes of RNA, detect point mutations in expressed transcripts, identify fusion transcripts or uncover new alternative splicing events.

Comments：Is this so called "point mutations in expressed transcripts" SNPs？

For this reason a number of researchers expect microarrays to migrate towards more targeted applications in the future, perhaps associated with biomarker validation or other diagnostic applications.

Direction of microarray.

Tree-Planting Day

Tree-Planting Day of this year. Remember to do a green thing today.

Pay attention to cytogenetics and procreation

A very promising field for health industry.Affymetrix SNP 6.0 can deal with both analysis of copy number & cytogenetics and SNPs.

理想

很高兴多少年理想一直在我心中，昨天又强烈点燃(mY gENE)！我坚信我要是坚定起来力量是可怕的，因为很早之前我就曾经领悟到第七感，虽然很难很难持久，但毕竟我做到过，只要我愿意我肯定能再次做到。所以最近把圣斗士星矢又从头到尾看了一遍，这个是团队作战和个人奋斗相结合必看的教育片，还能保持年轻的心。不过必须承认我还是喜欢黄金圣斗士，星矢这样的草根不是我的偶像，只是特例，很多事情当面的气质就已经盖棺定论了。

A breakthrough of synthetic biology.

"Brother" of systems biology,synthetic biology welcome his breakthrough to make self-reproducing synthetic ribosome, which is an important step in the quest to create artificial life forms. I almost forget that ribosome is the protein factory in organism. I can prospect a great promotion to biologic drug discovery than using bacterias.

George shocks me at a second time. I just wonder whether he will select me as one of volunteers in his personal genomics project.

很羡慕李白和唐寅之类的仙人，比较后我发现古人比今人接近仙境的几率要高很多！

赠诗一首：
桃花庵歌－－唐寅
桃花坞里桃花庵，桃花庵里桃花仙；
桃花仙人种桃树，又摘桃花换酒钱。
酒醒只在花前坐，酒醉还来花下眠；
半醉半醒日复日，花开花落年复年。
但愿老死花酒间，不愿鞠躬车马前；
车尘马后富者趣，酒盏花枝贫者缘。
若将富贵比贫者，一在平地一在天；
若将贫贱比车马，他得驱使我得闲。
别人笑我忒疯癫，我笑他人看不穿；
不见五陵豪杰慕，无花无酒锄作田！

弘治乙丑三月 桃花庵主人 唐寅

Resolve messy code problem of Chinese for SSH visit

Add information below into .bash_profile
export LANG=zh_CN.GB18030
export LANGUAGE=zh_CN.GB18030:zh_CN.GB2312:zh_CN

A great resource for brain expression

http://www.brain-map.org/

我爱虎扑

我爱虎扑，信陵公子张佳玮的散文真好看，分析真细腻，感觉到家乡的人文气息。同时做什么都要专业，那怕是玩！

生活小常识，来自爸爸。

利用个人一切可以利用的空间，同时穿插进行。
1、 大小便时咬紧牙关。
2、 每晚临睡前喝一杯牛奶，力争在11时前就寝。
3、 每晚临睡前在卫生间用较烫的水冲脚底、肚脐眼,同时用毛巾护住睾丸私处（以皮肤能承受为限）；用不太热的水冲洗私处和肛门，同时咬牙收腹提肛10次。
4、 每晚临睡前到一大杯开水冷却备用，早起时清水漱口；喝1升温开水；（夏天可喝凉开水）放较烫的水洗脸，用烫毛巾上下快速摩擦左右耳廓各10次，同时叩齿；用烫毛巾敷面1分钟后，迅速用凉水洗脸。早餐后刷牙。
5、 散步的同时上下左右转动眼球，同时可伴握力器或健身球手部运动。
6、 身边有座机时，不用手机打电话。
7、 根据自身的实际，建议每晚临睡前10点半左右定时大便，然后执行第三条。
8、 看电视时，可左右手相互摩擦若干次，掌心发热后放在耳朵上，重复三五遍。
9、 就餐吃大荤后，吃1粒核桃，吃一角萝卜。
10、 每天早餐吃几片生姜，中午12点后绝不吃生姜。

GG H1 and JETTA

GG H1: Glue Grant H1
A new human transcriptome array for clinical research designed by Stanford University and Affymetrix.

"This array enables comprehensive examination of multiple mechanisms human cells use to regulate transcriptome in response to diseases including improved analysis of gene expression with completely updated gene annotations and carefully redesigned probes, genome-wide quantitation of gene isoforms and identification of alternative splicing, coding and UTR SNP detection and allele specific expression analysis, examination of non-coding transcription and antisense expression, and the analyses of small RNAs.
"

Two significant features:
Software for gene and alternative splicing analysis (JETTA) and visualization
Using exon and junction probes in alternative splicing and isoform analysis
Study of unannotated transcribed units

JETTA is improved and integrative software of some algorithms developed by Wong group for exon array. But it should have more function to deal with non-exon probes, for example junction probes etc. I expect a version of JETTA for Linux in the future.

Anyway, I should admit that GG H1 is a powerful tool to investigate the transcriptome systematically. I just wonder if the hybridization for all of the probes on different regions is uniform. I think the SNPs are detected in DNA level, while splicing and miRNA in the RNA level. How can GG H1 identify all these genotypes in a single array? Anyway,comparing with tilling array, what is the advantage of GG H1? Is it worthy to develop an entirely new product with the existence of exon array and tilling array?

Reference:
http://gluegrant1.stanford.edu/~junhee/JETTA/instructions.html

The reader

Kindle 2, a very cool reader.
It can store 1,500 books; it can go for up to two weeks without a battery recharge; it has a crisper screen.

One must understand simple methods before trying to grasp more complex ones.

One must understand simple methods before trying to grasp more complex ones.

Be even!

Taste the feeling.

在天天向上看到一个非常有意义的东西。

健康产业包括哪些范畴？体检、健身、保健、疾病预防.... 都很有意思，以后注意积累学习。刚才看到一个提肛和辟谷术，一般人看了第一反应是“真TM扯蛋”，另一类觉得“真TM好玩”，第三类在想“会不会是真的啊？”。还有第四类人，就是我，但是我不告诉你们我在想什么。

又顺便扯一下另一个不相干的社会问题，现在的年轻人对中国文化的态度真的太漠然，对社会和政治真的太漠然。“大史纪”里面有一句经典的话：“谁TM给的钱多，我就给谁干”。那些颓废堕落的就不提了，剩下的用全副西方思想和技术武装的一些自我感觉良好的正太们也稍显肤浅。对Microsoft和Google崇拜得跟亲爹妈一样，自以为懂了会用了他们的一些产品，觉得很时尚，很power。真该让老江来好好教育教育：“naive，too naive！”现在中国文化变成了非主流，就像SM一样的地位，尴尬不？

我觉得每个人在思考自己合适做什么时应该内涵外延再广一点，就是这点感想。

码字端一下自己的心态

这两天挺奇妙的，其实很多事情都很顺，但是心绪上却不顺利，BT自己一下。有些事情这样想就误入歧途了。人又不为别人活着，为自己和家庭，如果将来有出息了再为回馈社会。人也不一定要和谁比，人比人气死人直白点讲就是气死自己。再次让我意识到唯心主义的重要性，经过D的错误教育，这个词目前很多时候被认为是贬义词，我要为它拨乱反正。

以前我一直是坚定的唯物主义者，但是我觉得在现今的中国就是太马列唯物主义了，变成了唯物质主义。人之初，性本善，TNND都被生活压力变得虚伪、自保和自私。我不知道是不是大多数人明白了人生的意义。我看到一些不同阶层的人在享受人生的快乐，真的有时不是用金钱来衡量的。但是我也看到一些所谓的高地位、富豪或者著名学者自欺欺人地在生活着。今天的一个会议让我懂了很多人，他们有的真的很善良，有的被社会“熏陶”了，当然了他们都没有错。今天唯一值得高兴一下的是我观察人的能力现在真的很强，我的感情真的很细腻，感觉真的很灵敏，在这方面具有leader的潜质。

我庆幸我快30岁时重新找到了生活的真谛，那是我17，18岁时曾经很接近过，但是被现实所剥离的东西。但是我又发现自己还是不成熟，不禁感叹十年前看过的一部电影里的一句歌词“How many roads must a man walk down?”。How many？

Some bioinformatics ID converters

They are very useful!

http://www.ebi.ac.uk/Tools/picr/
http://david.abcc.ncifcrf.gov/conversion.jsp
http://idconverter.bioinfo.cnio.es/
http://smd.stanford.edu/cgi-bin/source/sourceSearch
http://cbi.labri.fr/outils/alias/

I see the great power of life!

We all left office for a two weeks holiday of the Spring Festival. An ornamental was put close to the central heating and no water. When I was back to office, its leaves are perishing. What it is pity!
I water it immediately and hope it can survive. My feeling is blue for it.
But just two days, it is aglow with health. The power of life is great! We should understand this truth.

A marker for 2009！

A hopeful year for me and my family！

理想和现实的一些思考

作为一种社会型动物，我觉得人们多数需要的是种认同感，尤其是自己所在意的人们认同。所谓理想也多为立志获得这种认同感的目标与抉择，而现实的残酷就可理解为实施目标时对自己预估的偏差或反驳。至于你提到的那四种“理想“或说病态的表现，我看是每个人的阅历迥异让他们的价值观和衡量认同感的标准不同罢了。但是，无论如何，兴趣并不同于理想，但能合二为一无疑最优。实际上我们的兴趣也往往来自于自己的成就，或说自己在某方面的成绩得到了别人或自己的认可，进而有更大的动力主动去做，因此这样看，理想与兴趣也许并不矛盾，关键还是实现理想的过程与历练能否与各人的心理承受所匹配。共勉一下：机会远比安稳重要，事业远比金钱重要，未来远比今天重要。”

以上引用自：http://hustkiwi.javaeye.com/blog/224814

我自居太史公说两句：
理想啊，其实没那么神圣，就是做自己喜欢的事情，这件事呢对大家还有点儿用，就可以了。千万别为了理想而理想，别为了虚荣而理想。