Nozzle: a report generation toolkit for data analysis pipelines Nils Gehlenborg 1 , 2 , Michael S. Noble 2 , Gad Getz 2 , Lynda Chin 2 , 3 and Peter J. Park 1 , * + Author Affiliations 1 Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA, 2 Cancer Program, Broad Institute, Cambridge, MA 02142, USA and 3 Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX 77230, USA ↵ *To whom correspondence should be addressed. Received January 10, 2013. Revision received February 10, 2013. Accepted February 13, 2013. Abstract Summary: We have developed Nozzle, an R package that provides an Application Programming Interface to generate HTML reports with dynamic user interface elements. Nozzle was designed to facilitate summarization and rapid browsing of complex results in data analysis pipelines where multiple analyses are performed frequently on big datasets. The package can be applied to any project where user-friendly reports need to be created. Availability: The R package is available on CRAN at http://cran.r-project.org/package=Nozzle.R1 . Examples and additional materials are available at http://gdac.broadinstitute.org/nozzle . The source code is also available at http://www.github.com/parklab/Nozzle . Contact: peter_park@hms.harvard.edu
Advanced Technology Behind the Harmony Test http://www.ariosadx.com/for-providers/rep_617_v3_0812_web_pdf.pdf ============== Non-invasive prenatal detection of aneuploidy by targeted next generation sequencing http://www.birminghamgenetics2012.org/pdfs/spoken/tuesday/5.4.pdf Helen White Senior Clinical Lecturer National Genetics Reference Lab (Wessex) http://www.birminghamgenetics2012.org/pdfs/spoken/tuesday/5.4.pdf
文献出处： Gontcharova V., Youn E., Wolcott R.D., Hollister E.B., Gentry T.J., Dowd S.E. Black box chimera check (B2C2): a windows-based software for batch depletion of chimeras from bacterial 16S rRNA gene datasets . The open microbiology journal. 2010, 4: 47-52. Abstract: The existing chimera detection programs are not specifically designed for "next generation" sequencedata. Technologies like Roche 454 FLX and Titanium have been adapted over the past years especially with the introduc-tion of bacterial tag-encoded FLX/Titanium amplicon pyrosequencing methodologies to produce over one million 250-600 bp 16S rRNA gene reads that need to be depleted of chimeras prior to downstream analysis. Meeting the needs ofbasic scientists who are venturing into high-throughput microbial diversity studies such as those based upon pyrosequenc-ing and specifically providing a solution for Windows users, the B2C2 software is designed to be able to accept filescontaining large multi-FASTA formatted sequences and screen for possible chimeras in a high throughput fashion. Thegraphical user interface (GUI) is also able to batch process multiple files. When compared to popular chimera screeningsoftware the B2C2 performed as well or better while dramatically decreasing the amount of time required generatingand screening results. Even average computer users are able to interact with the Windows .Net GUI-based applicationand define the stringency to which the analysis should be done. B2C2 may be downloaded from http://www.researchandtesting.com/B2C2.
Small-world or Scale-Free Phenomena in Internet: What Implications for the Next-generation Networks? Zouhaer M’Chirgui Euromed Management, LAREQUAD, Department of Information Finance Domaine de Luminy, BP 921- 13288 Marseille cedex 9, France Abstract The paper examines the large-scale topological structure of the Internet in order to see whether the structure exhibits some features that lead Internet Services Providers to go aside further collaboration for the deploymentof next-generation networks. The results indicate the existence of positive signs or early stages of possible movetowards more cooperative relationships, mainly among . These findings have implications for thenext-generation networks policy and strategy, particularly the move towards strategic alliances after the recentphase of mergers and acquisitions. Internet.pdf Keywords: Next-generation networks, Internet, Alliances, Small-world, Scale-free, Internet services providers1. Introduction
if you're going to san francisco be sure to wear some flowers in your hair if you're going to san francisco you're gonna meet some gentle people there for those who come to san francisco summertime will be a love-in there in the streets of san francisco gentle people with flowers in their hair all across the nation such a strange vibration people in motion there's a whole generation with a new explanation people in motion people in motion for those who come to san francisco be sure to wear some flowers in your hair if you come to san francisco summertime will be a love-in there if you come to san francisco summertime will be a love-in there 朋友最近要去San Francisco进修学习，我突然想起了上研究生时，我们外教经常给我们播放的一首曲子。今天下载后，听了听，感觉还是很好。 外教是一位因为战争而留在中国的美国老人，他在学校的家，是一座小楼，他会说一些汉语，还有两位中国孩子。 时间已经过去很久了，不知老人现在状况如何？谢谢这位留在中国而从事英语教育的老师。
From Paul Collodi The zebrafish possesses several favorable characteristics including a short generation time, external fertilization and optically clear embryos that make it an excellent model for studies involving the early stages of embryogenesis. Despite these advantages, one deficiency of the zebrafish model is the lack of methods for targeted gene inactivation and the production of knockouts. We have been working to address this problem by developing gene-targeting methods using pluripotent embryonic stem (ES) cell and primordial germ cell (PGC) lines derived from zebrafish embryos. Methods have been established for the culture of zebrafish ES cells that possess the capacity to contribute to the germ cell lineage of a host embryo. The ES cell cultures have been used to generate transgenic lines of fish and we are currently working to use the cultures to introduce targeted mutations by homologous recombination and produce zebrafish knockouts. The ES cell cultures will enhance the value of the zebrafish model for studies of gene function. http://zebrafish.org/zirc/home/guide.php
China Pushes the ‘Internet of Things’ The Internet of Things," which merges cloud computing with radio-frequency identification, wireless sensors, and other forms of embedded intelligence to develop the next generation of networked "smart" devices, has become a buzzword in China, giving rise to investors' guides, articles in the popular press, and a slew of dedicated websites. Experts caution that China's prowess is limited and that leading research on the Internet of Things is coming out of Europe and the United States. But with strong government support and a huge interest in new technologies, China's influence is growing in the emerging field. 详细内容： Science-2012-Hvistendahl.pdf
http://broadcast.oreilly.com/2010/04/public-draft-of-next-generatio.html The Committee Draft (CD) of the new version of ISO Schematron is now available at the ISO/IEC JTC1 SC34 SC34 Website (PDF). In the JTC1 workflow, this is the version that National Bodies comment on over the next 3 months. You can send comments in too, for example to me (as editor) or NB participants of the WG1 and SC34 (such as Alex Brown, Francis Cave, Jiří Kosek, Murata Makoto and Mohamed Zergaoui) and the issue can be raised in NB comments: I already have included features and changes based on comments here and from the Schematron mail list. After the ballot, we resolve any comments and put out a Final Draft International Standard (FDIS) (which is not open, so to reduce drag from implementations of drafts that might work against late changes, and to reduce the chance of implementations claiming to implement a standard but actually implementing a draft.) Then this FDIS gets voted on again. So it now is looking like 1Q2011 before the new version gets on the books at earliest: five years between versions seems healthy. All the features of the CD are already in the popular skeleton implementation at www.schematron.com (which I maintain) which has superceded my old Schematron 1.5 implementation at Academia Sinica. Please use ISO Schematron for new projects. I have discussed many of the new features of the draft before, but I'll just summarize some again: Modularity : The 2006 standard had anincludeelement however it was not very useful: it just stuck the external XML file and fragment inline. The 2010 CD enhances theextendselement, which substitutes the contents of the located file and fragment; this simple macro mechanism allows containers without the complication of SD-style components . Properties : The 2006 standard was most interested in communications with humans, and successful at that. It did provide several facilities for annotating this information, such as therole,seeandflagattributes. However, I began to see many users wanting incorporate structured information for automated processing in the assertion text, violating the purpose of it. For example, people would make an assertionX1233:c.34:2009:The widget should have a silly name, and then have some home-make parsing mechanism to extract the messages. This was particularly true when the structured information had some generated information. So the new properties element has been created to allow a more powerful approach with better representation of the separate concerns. The CD has a new Annex L, which gives many examples of what properties can be used for. Properties also provide a way of adding non-Schematron constraints, such as CRDL character repertoire typing. XSLT2 and EXSLT : Schematron is not limited to using XSLT1, but the schemas can select which query language binding they use. The 2006 standard reserved several names for this purpose. The two most popular are XSLT2 and EXST, so the CD defines bindings for these. (There is also an informative example binding for STX, the streaming transformations, to encourage implementation.) Structure Variables : The 2006 standard only allowed an XPath expression as the value of aletelement. However, this meant that when you wanted to have a lookup table for information, for better modularity, you had to use an reference to an external document. So the CD follows XSLT and also allows the value of a variable to be given in its content, which could include any arbitrary element content. Support for Document Collections : The advent of the XML-in-ZIP formats has brought to a head the trend in XML away from single large documents towards smaller linked documents. But this changed has reduced the utility of validation: patterns may be distributed between documents! The 2006 standard already allowed thedocument()function, which allowed an assertion or variable to access information in an external document, however the rule contexts were always the document being validated. In the CD, thepatternelement may have adocumentsattribute that can have an XPath expression that evaluates to a list of URLs. The pattern is tested on each of these documents in turn. (I am really happy with this approach, because it strengthens the idea of a pattern as something that adheres to documents rather than merely being some kind of odd type mechanism that adheres to information items.) I suppose it might even allow patterns limited to particular branches, too, but I have not pushed this as a justification, but it might have some efficiency and phase benefits. On this last feature, there is a suggestion that the mooted ISO ZIP standard should provide a simple solution to the multiple-document XML-in-ZIP validation problem: a kind of reverse structure to NVDL which creates a temporary synthetic XML document containing the ZIP directory structure and any XML files put inline: this would allow a single conventional schema to validate the whole XML-in-ZIP document even with grammars, and it would interact with NVDL well. However, thesch:pattern/@documentsattribute would be useful in any case. So please feel free to make comments on the draft, even here in the comments section. Especially if you have come to any brick walls where something that you were expecting to be simple was in fact not supported very well by the standard. The new draft Schematron standard is now a massive 40 pages. My expectation is that the standard will continue to be available free from ISO. Pretty good bang per buck. (Special thanks to WG1 convenor Alex Brown for the typesetting.)
http://www.nature.com/news/2011/110629/full/474543a.html Give the new generation a chance Romain Murenzi wants more young scientists in the developing world to be given the same opportunity to build careers that he was. Romain Murenzi In 1982, I was a 23-year-old high-school teacher recently graduated in mathematics from the National University of Burundi, but I dreamt of earning a PhD in mathematics and physics and a professorship at a major university. I applied for a 'Bourse du Tiers Monde' from the Catholic University of Louvain in Belgium, but was rejected. One reviewer said: "He is a refugee from Rwanda. If he comes to Europe for a PhD he will never return. Africa will lose an excellent high-school teacher." The response was both complimentary and inadvertently dismissive, suggesting that both I and Africa would be better off if I stayed put. I applied again the following year, and was selected. Since then, I have held various university and research posts in both Europe and the United States, and from 2001 to 2009 I had the honour to serve as minister of education, science and technology of Rwanda. I have been thinking about my personal journey lately. In April, I became executive director of TWAS, the academy of sciences for the developing world. The academy, which is administered by the United Nations Educational, Scientific and Cultural Organization and funded by the Italian government, is dedicated to building scientific capacity and excellence in developing countries. Part of the TWAS mission is to address the needs of young scientists. And although I hesitate to draw general conclusions from an individual case, this tempts me to compare my own experience (and those of my colleagues a generation ago) with the situation today. First the good news. It is highly unlikely that reviewers would suggest a promising fellowship applicant should not move. Brain drain is now seen as best addressed without compromising an individual's desire to reach his or her full potential. Also, there are many postgraduate and postdoctoral programmes, increasingly based on collaboration between the traditionally poorer countries of the Southern Hemisphere. TWAS alone offers more than 300 fellowships each year, sponsored by Brazil, China, India, Kenya, Malaysia, Mexico, Pakistan and Thailand. But we cannot close our eyes to aspects of science in the developing world that have not changed fast enough. First, there is the growing gap between countries that are rapidly strengthening their scientific capacity and those that lag behind. Just six developing countries account for three-quarters of the scientific articles published by scientists from the developing world in international peer-reviewed journals. And China alone accounts for 30% of all papers by scientists in the developing world. Clearly, such imbalances have serious implications for scientists — and especially for young scientists — in countries that are failing to keep pace. Second, even for countries in which scientific capacity is growing, there remains a yawning gap between science and innovation. This has particularly serious implications for poor developing countries, where politicians need to regard sustained investment in science as a way of reducing poverty and increasing wealth. “We cannot close our eyes to aspects of science in the developing world that have not changed fast enough.” I believe that three major steps must be taken to help countries stymied by poor scientific and economic capacity. First, provide adequate training for the next generation of developing-world scientists. Without a critical mass of professors with PhDs, and doctorate-level research, there is no way that scientific capacity can be built, let alone flourish. Second, expand opportunities for scientific exchange with colleagues in technologically advanced countries. Growing numbers of fellowships are available, yet the total number remains small. Too many eager and able young scientists in developing countries continue to be denied opportunities. And third, young scientists from developing countries must be given broader opportunities to obtain research funds to continue their studies. Again, levels of funding are increasing, but not rapidly enough to meet the growing demand. Part of this funding can be derived from foreign donors, but part must come from the countries themselves. Rwanda spends 1.6% of its gross domestic product on science and technology. This benefits a wide range of institutions, including the National University of Rwanda in Butare and the Kigali Health Institute. To boost tertiary education in science even further, 70% of the loans available for higher education are reserved for students majoring in disciplines related to science and technology. Furthermore, Rwanda's efforts have drawn help from governments and funding agencies from across the globe. Global financial institutions and bilateral development agencies must devise more comprehensive strategies to integrate science and technology into their development efforts. And the governments of scientifically lagging countries must create and pursue policies centred on long-term capacity building in science, technology and innovation. With most of the world's young people coming from the developing world, the future of not just poor countries but the entire world will depend on support for its young scientists. It is vital that university graduates there are given the same opportunity that I was. Romain Murenzi is the executive director ofTWAS, the academy of sciences for the developing world, inTrieste,Italy.
Dr Stijn Mahieu Ghent University Archived topic page last updated on 16 July 2008 http://www.scitopics.com/Reactive_Magnetron_Sputtering.html Magnetron sputtering is a widely used PVD (Physical Vapour Deposition) technique to deposit thin films. This technique is based on the generation of a magnetically enhanced glow discharge , the so-called magnetron discharge . When a reactive gas is added to the discharge, it becomes possible to deposit compound materials. This process, i.e. reactive sputter deposition, has been recently reviewed in two papers . Both papers discuss in detail the reactive sputter process and its stability problems . Indeed, the addition of the reactive gas results not only in the formation of a compound on the substrate but also on the target or cathode surface . This can result in a sudden decrease of the deposition rate and an abrupt change in the partial pressure of the reactive gas , the so-called hysteresis or poisoning effect . Although both papers give an excellent overview of the reactive sputter process and the techniques to circumvent the hysteresis effect , recent experimental and modelling results show that several fundamental aspects concerning reactive sputtering have not been elucidated yet. One of the major problems of the reactive sputter process is its complexity . Indeed, to understand and describe this deposition process in all its details, a complete characterisation and description of the sputter process is necessary. More specific, the interaction between target processes , plasma processes , the sputter process and subsequent collisional transport of the sputtered particles through the gas phase and all substrate processes should be taken into account since all of them are related to each other. Attempts to obtain such a total description of the sputter process are ongoing in or research group . A good understanding of the reactive sputtering process is essential when tailoring the thin film properties. Indeed, several authors have shown that the plasma chemistry plays a crucial role in the development of the microstructure and the crystallographic orientation of the deposited thin films . It is beyond doubt that the crystallographic orientation and the microstructure influence a wide variety of thin film properties. For “simple” materials these relationships have been thoroughly examined. However, most of the new technological interesting materials have a complex chemical (and crystalline) structure . These multi-elemental materials allow to tune many parameters, including lattice constants, electronic band structures, and magnetic properties. References * W.D. Westwood, Sputter Deposition, AVS Education Committee Books Series, Volume 2, AVS (New York) 2003 (ISBN 0-7354-0105-5) * “Fundamental understanding and modeling of reactive sputtering processes” S. Berg, T. Nyberg, Thin Solid Films 476 (2005) 215-230 * “Control of reactive sputtering processes” W.D. Sproul, D.J. Christie, D.C. Carter, Thin Solid Films 491 (2005) 1-17 * “Target poisoning during reactive magnetron sputtering: Part I: the influence of ion implantation” D. Depla, R. De Gryse, Surf. Coat. Technol. 183 (2004) 184-189 (Link-) * “Modeling of the target surface modification by reactive ion implantation during magnetron sputtering” D. Depla D, Z.Y. Chen, A. Bogaerts, V. Ignatova, R. De Gryse, R. Gijbels, J. Vac. Sci. Technol. A22 (2004) 1524-1529 (Link-) *“Comprehensive perspective on the mechanism of preferred orientation in reactive- sputter-deposited nitrides” Y. Kajikawa, S. Noda, H.Komiyama, J. Vac. Sci. Technol. A 21 (2003) 1943-1959 * “Mechanism of preferential orientation in sputter deposited titanium nitride and yttria- stabilized zirconia layers” S. Mahieu, P. Ghekiere, G. De Winter, S. Heirwegh, D. Depla, R. De Gryse, O.I. Lebedev, G. Van Tendeloo, J. Cryst. Growth 279 (2005) 100-109 (Link-) * "Reactive Sputter Deposition" edited by D. Depla and S. Mahieu, Springer, 978-3540766629 (Link-) * "Biaxial alignment in sputter deposited thin films" S. Mahieu, P. Ghekiere, D. Depla, R. De Gryse, Thin Solid Films 515 (2006) 1229 (Link-)
Chinese and American Young Generation Confront a Same World by Yubao The world Chinese young generation faced is different from Americans? It is a little complicated to answer this question. I think there is no great difference there and on the contrary there is a tendency of convergence such as re-education trend, career desperation and reality unintelligent. Like most college graduate come back to school in the United States , Chinese graduates are coming with the same tide. While some of the college graduates just continued to pursuit a Ph. D degree. Maybe the young generation of America has more working experience, for they start work earlier and changing work more frequently. But we can see a tide of returning to Graduate school after the Financial Crisis. UnlikeRoger Bacon said at three hundred yours ago, scientia potentia est (Knowledge is power), the line between power and knowledge is becoming more and more indistinct. Ph. D is no more a guarantee to a decent job. Many young men do not have a clear expectation of their career development. You can find the same thing in America . As many Scenes in the film Sex and the City, Greens Anatomy and Gossip Girl, are considered as a reflection of job seeking, city living in USA . Interestingly you can discover the counterpart in Chinese films, like Du Lalas promotion, Hard Working. They present snapshots of harsh reality the Chinese young generation faced. More and more people lost a solid cognition to the realty and honesty sprits to themselves. Two decade years ago, young people would read classic literature, care about the democracy, pay attention to social issues, but all these things are just kept in middle ages memory and faint away in the 21 century. Now we just read bills and only care about money and pleasure. It is a hard thing to inspect and comfort the inside of our own. So we easily surrender to the fancy world without a thinking and cheaply traffic ourselves in the labor market. Many intellectuals think this is the root of all evil in the world. We confront a flat world and it makes people lost destination, struggling for survival in the Postmodernism time. It is reliable to meet someone in the other side of the Earth, but we are tightly confined in a network knitted by commodities and markets. Sooner or later, the old clich, the vast pacific and social ideologies are the boundaries between China and United states , will be replaced by a new topic as rising young generation in the same Arena.
It's worth watching, especially for those who were born in the 1980s. http://www.youtube.com/watch_popup?v=42E2fAWM6rA By Jonathan Reed If you cannot watch YouTube, try this site, which shows the writing (but I am unable to steal): http://www.killahbeez.com/2009/01/23/lost-generation/ If you still cannot read it, here it is. (I typed it myself; any typos?) I am part of the Lost Generation And I refuse to believe that I can change the world I realize this may be a shock but Happiness comes from within Is a lie, and Money will make me happy So in 30 years I will tell my children They are not the most important thing in my life My employer will know that I have my priorities straight because Work Is more important than Family I tell you this once upon a time families stayed together but this will not be true in my era this is a quick fix society experts tell me 30 years from now I will be celebrating the 10th anniversary of my divorce I do not concede that I will live in a country of my own making In the future Environmental destruction will be the norm No longer can it be said that My peers and I care about this Earth It will be evident that my generation will be apathetic and lethargic it is foolish to presume that There is hope. And all of this will come true unless we choose to reverse it. (Then you read backward...) Note: This concept is based on a political advertisement by Recrear, which you can view at http://www.youtube.com/watch?gl=CAhl=env=lFz5jbUfJbk or read what I copied down at http://www.sciencenet.cn/m/user_content.aspx?id=312537
标签: generation
