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JDIS Science Mapping论文公众号推介文章[胡志刚]
热度 5 ChaomeiChen 2017-4-6 10:24
胡志刚介绍了我在 JDIS 最新一期上发表的Science Mapping的文献综述。 新综述采用了一些CiteSpace里的新方法,也沿用了一些熟悉的方法。 胡志刚在介绍中还穿插比较了2012年和再生医学综述在宏观和微观层次上理论,方法和解读等方面的异同。另外,由于JDIS论文原文为英文, 胡志刚的这个中文介绍可能会对大家有所帮助,读起来也更方便。 微信网址: http://t.cn/R63KeOj 科学网: http://blog.sciencenet.cn/blog-43950-1043931.html 陈超美教授又一力作,你要的 CiteSpace 应用的完美范文来了~ 2017-04-06 胡志刚 大连理工大学WISE实验室 对于广大 CiteSpace 的学习者和使用者来说,怎么用 CiteSpace 来绘图,做出来的图谱怎么去用,怎么对这些图谱进行解读,是应用 CiteSpace 进行论文或报告写作的时候最常遇到的三个问题。 在最新一期的 JDIS (Journal of Data and Information Science)中, CiteSpace 的开发者、大连理工大学长江学者讲座教授陈超美博士,以一篇教科书式的完美范文,向我们展示了 CiteSpace 工具怎么用,CiteSpace 论文怎么写。 ...... Chaomei Chen (2017) Science Mapping: A Systematic Review of the Literature. Journal of Data and Information Science, 2017, 2(2): 1-40. DOI: 10.1515/jdis-2017-0006 http://www.jdis.org/10.1515/jdis-2017-0006 或者用ResearchGate: https://www.researchgate.net/publication/313991204_Science_Mapping_A_Systematic_Review_of_the_Literature
个人分类: CiteSpace应用|8151 次阅读|10 个评论
[文献综述/Expert Review]: Science Mapping
ChaomeiChen 2017-3-16 17:20
Chaomei Chen (2017). Science Mapping: A Systematic Review of the Literature. Journal of Data and Information Science, 2(2), 1-40. DOI: 10.1515/jdis-2017-0006 http:// manu47.magtech.com.cn/ Jwk_jdis/EN/abstract/ abstract8643.shtml
个人分类: CiteSpace应用|6354 次阅读|0 个评论
二代测序短序列mapping新选择:Magic-BLAST
热度 1 mashengwei 2017-3-3 17:47
Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. 前面一段 时间看到NCBI上blast出了一个新系列,短序列的mapping。基本与blast使用体验一致。Magic-BLAST 也适用于长片段mapping,比如EST。最好调整默认的参数。 科学网博客排版不是很好,详细参见 二代测序短序列mapping新选择:Magic-BLAST 1、下载 官网下载(ftp://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/LATEST) 我下载的是编译之后的,下载之后将magicblast和makeblastdb拷贝至系统全局变量路径即可。 2、使用 对经常使用blast的人来说使用非常简单。甚至不用将reference序列建库,直接使用fasta格式的序列文件即可。比如: magicblast -query SRR1228245_1.fastq.gz -query_mate SRR1228245_2.fastq.gz -infmt fastq -subject ref.fa -outfmt sam -out SRR1228245_blast.sam -num_threads 10 -splice T 其实,如果前面使用过makeblastdb将参考基因组建库,magicblast可以直接使用。比如 magicblast -query SRR1228245_1.fastq.gz -query_mate SRR1228245_2.fastq.gz -infmt fastq -db /data2/Fshare/IWGSC_v1.0_Formatdb/CS_v1.0_full -outfmt sam -out SRR1228245_blast.sam -num_threads 10 -splice T #如果是DNA_seq ,需要将 -splice 设为 F 支持的输入格式 SRA, FASTA, FASTQ, or FASTC 等。在NCBI上下载的SRA序列这次可以直接使用了😝。当然支持压缩格式 .gz。 输出格式支持sam, tabular, asn。 更多的其他用法这里就不在啰嗦了,请参见下面的README已经help
6921 次阅读|4 个评论
中国动态地图——Mapping China V1.2-20140528
热度 2 myvolcano 2014-5-15 13:13
Mapping China简介 中国动态地图——Mapping China可以在按省份划分的中国地图上显示用户给定的指标数据,并用不同的颜色对不同的数据范围加以区分,可用于研究某种资源的全国地域分布及各省份之间的对比等。 Mapping China V1.2 主要更新:(1)对Mapping China进行优化处理;(2)对使用说明进行较大改进。 欢迎各位试用,并提宝贵建议! Mapping China运行环境 经测试, Mapping China V1.2 可以在 Windows 7 与 Windows XP 操作系统中正常运行。 运行 Mapping China V1.2 前,请务必确认以下事项: ( 1 )正在使用的电脑上已经安装了 Adobe Flash Player 。如果还没有安装,请到官方网站( http://get.adobe.com/cn/flashplayer/ )下载、安装最新版本的 Adobe Flash Player 。 由于 Windows 8 对 Adobe Flash Player 的支持存在一定问题,因此 Mapping China V1.2 在 Windows 8 系统中可能无法正常运行。 ( 2 )将下载后的压缩文件(例如“ Mapping China V1.2-20140528.rar ”)中的 “ Mapping China ”文件夹解压到 D 盘根目录。解压后,可以看到以下文件: Mapping China V1.2.pdf (文件路径必须为“ D:\Mapping China\Mapping China V1.2.pdf ”,下同。) Mapping China V1.2 使用说明 .pdf ProvinceDada.xml ProvinceDada.xls Foxit Reader V3.0.rar (解压后为“ Foxit Reader V3.0.exe ”,一款 PDF 文件阅读器,绿色、单文件版,无需安装,双击直接运行。) 某些 PDF 阅读器对 Flash 的运行支持不是很好。如果“ Mapping China V1.2.pdf ”无法正常运行,请尝试先运行“ Foxit Reader V3.0.exe ”,然后从该软件中打开“ Mapping China V1.2.pdf ”。 更多详情,参见附件中的 MappingChina V1.2 使用说明! 致谢 Mapping China的研究工作得到国家社科基金项目(13CTQ025)的资助。 **作者 您在使用Mapping China过程中,如果遇到什么问题,或有什么意见/建议,都欢迎致信matc@mail.whlib.ac.cn,与作者进行**。 附件 (文件大小:3.49MB,解压密码:whlib) Mapping China V1.2-20140528.rar
个人分类: 交流分享|8956 次阅读|3 个评论
WMS-Based Flow Mapping Services
guodanhuai 2012-9-13 09:33
ABSTRACT Flow Mapping, also known as spatial interaction data visualization, has become widely used for exploratory spatio-temporal data analysis to understand complex spatial phenomena such as human migration, commercial trading, and social networks. The unitary flow mapping architecture, in which data storing, computing and representation are deployed in a single computer, is facing the challenges being brought from increasing data scale, higher timing demand, computing complexity of visual clutter detecting and integrating with other GIS and spatio-temporal analysis tools. In this paper, a novel 3-tiers flow mapping service architecture is proposed. In this architecture, flow data integration tier provide a unified data access interface for variant data sources; flow mapping models tier provide a computing resource pool to support different flow mapping algorithms and scalable computing capability; and result visualization tier to view map interactively. In this paper, we expand the OGC Web Map Services(WMS) standard protocol to support spatio-temporal interaction data visualization and analytics, and integrate WMS-based flow mapping service with other map resources by JavaScript toolkits in browsers. This architecture is validate to be improved in performance and scalability by three typical application cases. 1. Guo, D., et al. WMS-Based Flow Mapping Services. in Services (SERVICES), 2012 IEEE Eighth World Congress. 2012. 全文下载: WMS-based FM services.pdf
个人分类: GIsystem & GIscience|4211 次阅读|0 个评论
我为博士课程考试学的新一代测序技术总结!
热度 5 lry198010 2011-4-12 17:25
我为博士课程考试准备的新一代测序技术总结 (新一代测序技术的序列分析方法及在油菜基因组研究中的应用.docx )!很多地方可能不对或考虑不周到,欢迎大家提出批评意见。
个人分类: 生物信息|5030 次阅读|3 个评论
ECDL2010上的NKOS Workshop
xuechunxiang 2010-9-3 10:22
一直关注NKOS的研究东西,在即将召开的ECDL2010会议上,今年NKOS的主题是关于Mapping、SKOS、link data。参与者都是每年NKOS会议的老面孔啊,议题也延续了往年!期望等资料公开后能看到KOS的一些新内容。 Networked Knowledge Organization Systems and Services The 9th European NKOS Workshop at the 14th ECDL Conference, Glasgow, Scotland Thursday 9th (start 2:00pm) Friday 10th (finish 1.30pm) September 2010 议程安排:Workshop Programme (Venue: BO Theatre A) Thursday 9th September 14.30 15.00 Welcome and introduction to workshop and participants (Doug Tudhope) Session 1: Mapping, mapping relationships and retrieval performance Chair: Vivien Petras 15.00 15.30 Antoine Isaac. Progress in semantic mapping 15.30 16.00 Stella Dextre Clarke. Types of mapping recommended in ISO 25964, and the question of reciprocity 16.00 16.30 Coffee break 16.30 17.00 Mapping discussion 17.00 17.15 Felix Boteram. Stratified semantic relations: Information retrieval and knowledge exploration in distributed knowledge organization systems 17.15 17.45 Philipp Mayr, Peter Mutschke, Philipp Schaer, York Sure. Search term recommendation and non-textual ranking evaluated 17.45 18.30 Demonstration session (using participants own laptops) The session will be followed by the usual informal evening dinner where discussions can continue. The venue will be announced at the workshop. Friday 10th September Session 2: User centred KOS design and evaluation Chair: Stella Dextre Clarke 09.00 09.30 Anna Mastora and Sarantos Kapidakis. Users and KOSs: When Can We Trust Those Two Together for Conceptual Query Expansion? 09.30 09.45 Louise Spiteri, Laurel Tarulli, Alyssa Graybeal. The public library catalogue as a social space: Transaction log analysis of user interaction with social discovery systems 09.45 10.00 Hugo Manguinhas, Jos Borbinha. Integrating Knowledge Organization Systems Registries with Metadata Registries 10.00 10.15 Margie Hlava. Using KOS as a basis for text analytics and trend forecasting 10.30 11.00 Coffee break Session 3. SKOS and linked data Chair: Antoine Isaac 11.00 11.15 Gudrun Johannsen, Ahsan Morshed, Johannes Keizer, Gudrun Johannsen, Armando Stellato, Thomas Baker. Towards AGROVOC OWL Model to AGROVOC SKOS Model 11.15 11.30 Johannes Hercher, Harald Sack. Indexing Audiovisual Heritage in Germany by SKOSification of Existing Vocabularies 11.30 12.00 Ceri Binding, Doug Tudhope. KOS-based tools for archaeological dataset interoperability 12.00 12.30 Riccardo Albertoni, Monica De Martino, Franca Giannini. SKOS and semantic web best practice to access terminological resources: NatureSDIPlus and CHRONIOUS hands-on experience 12.30 13.00 Thomas Schandl, Andreas Blumauer, Helmut Nagy. Using Linked Data in Thesaurus Management 13.00 13.15 Conclusions
个人分类: 我思我在|4826 次阅读|0 个评论
vector field
guodanhuai 2010-3-24 16:31
In mathematics a Vector field is a construction in vector calculus which associated a vector to every point in a subset of Euclidean space. Vector fields are often used in pysics to model, for example, the speed and direction of a moving fluid thoughout space, or the strength and direction of some force, such as the magnitic or gravitational force, as it changes from point to point.
个人分类: Notes & Plan|3736 次阅读|0 个评论
[转载]科学计量学研究报告(OA)January 27, 2010 Mapping Change in Large Networks
xupeiyang 2010-1-29 07:40
Martin Rosvall 1 * , Carl T. Bergstrom 1 , 2 1 Department of Biology, University of Washington, Seattle, Washington, United States of America, 2 Santa Fe Institute, Santa Fe, New Mexico, United States of America Abstract Top Change is a fundamental ingredient of interaction patterns in biology, technology, the economy, and science itself: Interactions within and between organisms change; transportation patterns by air, land, and sea all change; the global financial flow changes; and the frontiers of scientific research change. Networks and clustering methods have become important tools to comprehend instances of these large-scale structures, but without methods to distinguish between real trends and noisy data, these approaches are not useful for studying how networks change. Only if we can assign significance to the partitioning of single networks can we distinguish meaningful structural changes from random fluctuations. Here we show that bootstrap resampling accompanied by significance clustering provides a solution to this problem. To connect changing structures with the changing function of networks, we highlight and summarize the significant structural changes with alluvial diagrams and realize de Solla Price's vision of mapping change in science: studying the citation pattern between about 7000 scientific journals over the past decade, we find that neuroscience has transformed from an interdisciplinary specialty to a mature and stand-alone discipline. Citation: Rosvall M, Bergstrom CT (2010) Mapping Change in Large Networks. PLoS ONE 5(1): e8694. doi:10.1371/journal.pone.0008694 Editor: Fabio Rapallo, University of East Piedmont, Italy Received: November 20, 2009; Accepted: December 17, 2009; Published: January 27, 2010 Copyright: 2010 Rosvall, Bergstrom. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by the National Institute of General Medical Sciences Models of Infectious Disease Agent Study program cooperative agreement 5U01GM07649. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing interests: The authors have declared that no competing interests exist. * E-mail: rosvall@u.washington.edu 原文见: Mapping Change in Large Networks
个人分类: 信息分析|2024 次阅读|0 个评论
Research note of Experiment in migration by computer
guodanhuai 2009-12-10 14:56
The areas between migration, or other movement, occurs are connected by a band whose width represents the quantity moved. 1)Ideally a desirable parsing strategy is one which yields only a linear growth in the number of movements needing to shown. Wherei the geographical space is considered to be continuous, not broken into data collection units, and the table no longer finite. This lead one to methods of movement depiction more analogous to those used in fluid dynamic. These continuous techniques are also useful for movement tables of large but finite size although the present discussion is limited to more conventional mapping methods. 2) The ealiest computer drawn flow maps are those of the Chicago Area Transportation Study. A special cathod ray tube system, the cartographatron, was constructed to display several million desire lines. 3)In addition to the computer N by N movement table, one is required to have a map showing the boundaries of the data collection on the movement map. Weighted geographic centroids of these regions are calculated and used as rectangular coordinates for the initial and terminal points of the flow lines. a small offset from these origin-destination points is generally desireable in order to avoid excessive overlap where flow bands come together. a) The simplest graphic is the rectangular flow band with width proportional to the flow and stretching from starting centroid to ending cetroid, and representing all of the two-ray flow from place A to place B and from place B to place A, a combined total. it is necessary to choose a scale of flow magnitudes, and this choice clearly impacts the impression obtained from the map. As a default option, convenion but not necessarily correct, the computer program fixes the width of the largest flow band, making it equal to the distance between the closest centroid pair on the map. b) Should the width of the flow band be proportional to the magnitude of the movement? One alternative is to make all flow bands the same width, and then to use a variable intensity shading to represent the magnitude, as on choropleth maps, or to use a color variation to indicate the intensity of movements. Alternatively, the shading density times the area shaded (length times width of band) can be made proportional to the movements, this option corresponding to the notion that visual intensity should be proportional to density times area. Or the bands can be chosen to have their area(width times length) proportional to the movement magnitudes, the idea again being that eys responds to area and not just width. c) In order to be able to represent the movement from place A to place B as something distinct from the movement in the reverse direction we require an asymmetric symbol, the flow arrow being the classic form. Generally there will be N*(N-1) of these, when the self-moves are omited. difficult graphical problem, not really solved. --A major difficulty lies in showing the simultaneous two directional movement along the single path coonecting places A and B. Half-barbed arrows, each of whose width is proportional to the respective movement, which about or which are separated by a small gap, do not seem very effective visually, nor does putting the smaller flow arrow on top of the larger one work very well. --Another difficulty stems from the First Law of Geography, near places interact more than distant places. Thus the large movements are often between close places on the map, where there is little room to draw anything. A common cartographic technique used to overcome this problem is to choose a base map, which enlarges area of high areas of high data density. --The graphical simplicity of the maps is greatly enhanced if the arrows or bands are shown with overlap deletion. The intitial guess was that we should have arrows representing the smaller flows cress over the top of the larger flows. The reverse in fact seems prefered. WHY? The map clutter seems reduced for a given size of from-to table, and the more important (larger) movements become more noticeable. d) The number of migration, which need to be shown, can be reduced in a number of ways. (1) Instead of showing the entire N-squared possible migrations on one map, all of the N-1 movements from one place, or to one place, can be shown, in gross or net form. These possibilities will yield 4N distinct maps from one single N by N from-to table. (2) Another, classical, method is to delete all of the movements below some threshold quantity. The problem lies in determing this threshold level. The optinal deletion strategy is to remove all movements whose magnitude is less than that of the average table entry. This delecately balances the deletion of individual migration streams with retention of movement volumes. (3) Arbitrary thresholds can now be relaced by the optimal cut-off value, and this simple rule greatly reduces the map clutter while still providing a faithful representation of the geographic situation. An alternative is to use a theoretical model to produce a table of expected movements and then to show only those movements which are significantly different from these expectations (4) Collapsing a migration table to a smaller size by combining adjacent (geographically contiguous) place is a common technique. If it must be done it probably should be done in such a manner as to reduce the variance of the resolution. (5) Simplifying a from-to table can also be done by allowing movement to take place only between geographically adjacent places. (6) Instead of drawing arrows from centroid to centroid an interesting variation would now be to place the arrows to just cross the borders of the immediately adjacent regions. Open serveral research problems: 1. Spherical nature of the earth being taken into account From a computational point view it is immaterial whether the data table is of within-city movements, or between the provinces of a country, or between several countries within a region, but truly international movement is different because the spherical nature of the earth has not been taken into account. One can imagine drawing the flow arrows along great circles on an oblique orthographic view of hemisphere; the map projection problem becomes even more difficult when a movement pattern over the entire world must be shown. 2.The migration data is often desired to look at the difference between two tables, at distinct time period, or for populations partitioned by age, sex, or other charateristics, or to compare a theoretically computed table with an observed table. 3. Finally, completely different display techniques seem called for in more dynamic situations when one has a movement table which is regularly updated; by decade, by year, or by month. Real cartographic animation 4. Commuting data also lend themsleves to this type of depiction. converting residental street addresses into geodetic coordinates, and combining this with resent advances in high volume data storage and processing capabilities. Point-to-Point rather than area-to-area movements are more expected.
个人分类: GIsystem & GIscience|3266 次阅读|0 个评论
GMT 及Win4GMT简介及其安装技巧
热度 1 kiger 2009-9-19 17:17
GMT-The Generic Mapping Tools ,即通用制图工具,是一个开源的工具集,主要用于 XY 和 XYZ 数据的处理和显示,包括栅格化、过滤和各种地图投影等操作。 GMT 最初是由哥伦比亚大学的两位毕业生 Paul Wessel 和 Walter H. F. Smith 于 1988 年创建的,至今已经发展到版本 4.5.0 。 经过这段时间的了解,感觉该软件主要有以下几个优点:( 1 )完全免费;( 2 )源代码是开放的,可以进行二次开发;( 3 )可以在多种系统下安装和使用,如 UNIX , Linux , MkLinux , Mac OS 9 , Windows 和 OS/2 ,但是每个系统下的安装要求是不一样的;(4) GMT 好比一个工具箱,每个工具之间相对独立,操作起来更为灵活,这也是 GMT 研究小组的一个特别考虑;( 5 )有很多免费数据资源都可以被 GMT 调用,尤其是 NOAA , USGS , NGDC , NEIC 等;( 6 )制作出来的图形图像精美,感觉比 ArcGis 和 MapGis 等软件成图的效果要好。正是由于以上诸多优点,该软件已经被较为广泛应用于医学,工程,物理,数学,地球科学,社会科学等领域。 由于该软件的最初是在 UNIX 系统上发展的,所以对于初学者来说早期的版本安装和使用方面还是有点麻烦的,我也是学习第一次安装该软件,经过摸索,终于在 Windows XP 系统下安装成功。习惯了 Windows 操作的人来说,突然要用 DOS 操作,确实需要一段时间的适应,故可以安装一个 GUI (图形交互界面)软件 Win4GMT 。具体安装过程如下: 1. Install GMT 3 (E g : C : \GMT\ ) . As you will see GMT3 programs will be installed in C : \GMT\ bin and rivers, border, shorelines, patterns etc in C:\GMT\share\coast and gmtenv.bat in C : \GMT\ ( Note: I n GMT 4 .5.0 , gmtenv.bat cant be need any more, and the installer has done the work and set the path. ) 2. S et Home: Modify gmtenv.bat with an ASCII editor in order to set your home dir . SET NETCDF= C : \GMT\ SET GMTHOME= C : \GMT\ SET HOME= C : \ USERS \ USERS \ PROJECTS or C :\ GMT \ TEMP SET PATH=%PATH%; %GMTHOME%\BIN; %NETCDF%\LIB 3. R un cmd command to open this window i n a DOS window . I n GMT 4 .5.0 , .gmtdefaults is created by default in C : \ GMT \bin, you should copy it to C : \GMT\. Then c lose the window . 4. if necessary, install Ghostsview or other postscript viewer or editor . 5. Put netcdf.dll in C : \GMT\. 6. Unzip the Win4GMT and r un setup.exe to install it . To avoid problems , Please install Win4GMT in the GMT Home Directory ( C : \GMT ). 7. Reboot the computer . 8. Configure folders in Preferences menu when starts the program or edit win4gmt.ini in C:\WINDOWS or C:\WINNT folder . Notes: Setup will create a subdirectory ( man ) where will be installed the html version of the GMT manuals. If you have problems with OLEAUT32.DLL (in some cases, problems has been reported) . R ename your oleaut32.dll (just in case) and copy the ftp file in your system directory ( C : \WINDOWS\S ystem) . Then r estart the computer. 其它: GMT下载地址: http://gmt.soest.hawaii.edu/ Win4GMT下载地址: http://www.icm.csic.es/gma
个人分类: 学研心得|11918 次阅读|3 个评论

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