BioInfoServ OS

Specially for BioScience and Home using



bioinfoserv


本手册基于Ubuntu/Xubunt和hiweed-linux Desktop帮助手册改写，版权归 © 2004, 2005, 2006, 2007, 2008 Canonical Ltd.（Canonical有限公司）、Ubuntu、© 2006， 2007，2008 HiweedLinux和© 2006， 2007，2008 BioInfoServ Team文档项目成员。关 于BioInfoServ OS更多细节，可查看http://www.bioinfoserv.org
1.系 统说 明
2.系 统安装手册
3.windows 系统与BioInfoServOS软件对应列表
4.BioInfoServOS定制教程
  1. 生 物软件

  2. 办 公系统

  3. 图 形与文档阅读

  4. 多 媒体和光盘工具

  5. 下 载工具

  6. 网 络工具

  7. 聊 天沟通

  8. 桌 面搜索

  9. 系 统管理

  10. 系 统安全

  11. 站点服务

  12. 跨 平台

  13. 其他软件和应用环境

软件特性说明
(亦可查看Windows 系统与BioInfoServ OS系统软件对应列表）

1.办公系统

      系统建议您使用openoffice.org和永中office2007（若 未安装请自行安装，在终端命令窗口下：sudo apt-get install openoffice.org*即可自动完成安装。另外，程序菜单中提供了“办公套件”菜单，您只需要点击这个 菜单，就能自动完成这两个办公工具的安装），较好地解决了Linux下的办公软件体系，而且它们可以很好地和 microsoft office兼容互访。当然，linux下的办公软件有很多，您完全可以自行选择，不过系统默认的办公软件，可以说是目前最优秀的linux办公软件组 合，它们高度兼容windows下的Office软件，基本可以让您摆脱对MicroSoft Office的依赖了。此外，您如果有良好的网络状态，还可以使用在线办公软件GoogleDocs。   
      对于简单的文本编辑，您可以使用Gvim, Mousepad, geditor等，它们比windows下的Notepad不知道好到那里去了。

2.图 形、文档阅读工具

   图像处理软件：gimp2.0,  如果您觉得windows下的Photoshop不错，您完全可以下载一个绿色软件运行包，然后采用hiweedlayer, CrossOverOffice和EasyWine来运行。而且您还可以安装GimpShop，这个几 乎完全具有Photoshop的界面。
   作图工具：Draw diagrams, Freemind， xfig；
   图片管理 工具：picasa, F－spot, Picasa；
   图 片快速浏览工具：GQview（这个相当于windows下的ACDSee)；
   抓图工具：Ksnapshot；
   颜色拾取 工具：Gcolor2；
   在线帮助 文档阅读器：Chmsee；
   PostScript 和PDF阅读器：Evince，当然您AcrobatReader for Linux也是很好的，而且系统中还有一个免费的PDF阅读软件FoxitReader，也是非常好的，这些系统已经默认安装。
至于其他 一些特殊图形处理、绘制和文档的阅读器，可能需要您自己寻求解决方式，您可以在系统的软件仓 库中使用graphic, figure，3d关键字段进行搜索（如在终端下的搜索命令是apt-cache search graphic），看软件仓库中时候有您需要的相应软件，像QcomicBook阅读漫画书籍。

3. & nbsp;多媒体、光盘工具 

   媒 体中心软件：vlc;
   多功能播放器：mplayer；    
   电影播放器：totoem；    
   音乐播放器：beep；
   光盘文件编 辑工具：isomaster；
   光盘烧制工 具：gnomeBaker, k3b, NeroLinux (它的使用SN可以采用windows下的nero 6.0的SN，系统默认的版本为2.1.0.3，其SN可以采用1A23-0017-8035-2423-2521-3252）
   桌面录制软 件：istanbul； 
   视频录像工具：dvr-qt

4. 下 载工具

    多线程下载工具：Mutiget， prozigui；
    网页镜像工具： wget，Grsync；
    FTP下载工具：FileZilla， GFTP
    BT 下载工具：, amule, Azureus, Bitsrorm lite BT

5. 网页浏览器和网络电视软件以及校园网认证工具

   firefox, Mozilla web broswer，gtk-soapcast
    此外，针对校园网所采用的客户端认证工具，您可采用wine技术的来运行Dr.com，它可以让您轻松适应这种特殊网络状态的需要。

6. 聊天沟通工具

   QQ软件：Lumaqq, eva 
   多协议聊天工具：Gaim, Kopete
   GoogleTalk: Tapioca Gtalk 
   网络电话：skype, WengoPhone, Ekiga
   IRC频道：XchatIRC

7. 桌面搜索工具

   基于cache的桌面搜索工具：beagle
   即时指定文件夹搜索工具：SearchMonkey

8. 系统管理工具

   系统启动管理工具：bootup-manager，sysv-rc-conf
   系统进程管理：process manager, gnome-system-monitor
   系统清理工具 ：kleansweep, remove orphaned packages
   分区管理工具：gparted
   磁盘文件恢复：dares, photorec
   磁盘镜像 ：partimage
   文件备份：unison
   字体管理 ：dfontgr
   系统光盘制作：UbuntuCustomizationKit， reconstructor
   系统配置文件编辑器：xorg-edit，这 是一个图形化的系统硬件驱动配置文件工具
  系统启动和运行优化：系统已经默认采用pre-load来优化管理系统的启动和运行速度，如果您还是觉 得系统运行比较缓慢的话，您使用 sysv-rc-conf依 照http://www.ubuntuforums.org/showthread.php?t=89491的 指导来进行。

9. 系统安全

 防火墙：firestar
   杀毒软件：avast! （使用授权书可以去http://www.avast.com/免费申请，申请一次可以使用1年）
10. 站点服务
 Apache2+MysqlServer5.0+MysqlClient5.0+Php5+PhpMyqdmin2.8.1： 这个网页运行环境是黄金组合，安装这个很简单：
sudo apt-get install apache2 phpmyadmin mysql-client-5.0 php5-mysql
安装配置过程会自动完成，只是在mysql配置过程中，会提示配置管 理密码。对于mysqlserver的管理，您可以使用phpmyqdmin，在浏览器里键 入 http://localhost/phpmyadmin，回车就可以看见很简单有效的数据库登录界面，帐户为root，密码为空（如果您觉得可以使用它 提供web服务，请您设置密码）。当然，管理mysql数据库，您还可以使用系统工具的“MySQL Administrator"图形化管理软件。

Apache2的配置文件在/etc/apache2下，Mysql的配置文件在/etc/mysql/my.cnf, php5的配置文件在/etc/php5下, ，您可以依据自己的需要来进行相应的配置。至于相关的配置教程，可参考http://www.oac.uci.edu/X/W6/httpd-howto/httpd.conf.d.html（apache 配置文件解释）。

  gproftp， 这个FTP服务默认安装，但是没有进行启动，请您在配置后进行启动，GproFTP的配置文件为/etc/gproftpd/gprotls.conf。

上面的 网络服务系统.，您完全还可以用它建立对外的站点服务，不过，在提供服务时，请您修改相应的设置以保障站点安全。另外，您可以使用xoops 2.0.16来建立自己的发布网站。对于xoops，您可以参考www.xoops.org。对于xoops 2.0.16，您可以采用以下命令来快速获得安装：
sudo apt-get bioinfoserv-xoops-2.0.16
安装完毕，您可以打开浏览器，输入地址http://localhost/bioinfoserv登 录，帐户和密码为admin/admin。如果要增加站点的功能模块，你只需要去http://xoops.org.cn下载相应的 功能模组，然后解压放到/var/www/bioinfoserv/modules/下，然后再登录网站的管理区，进行安装就可以使用了。

对于网站对外提供服务是需要域名和端口和映射的。如果您有域名，那么请修改/var/www//mainfile.php这个文件，把define ('XOOPS_URL', 'http://localhost/bioinfoserv');中的localhost换成您已经申请的域名就可以了。当然，如果您没有，您完全可以 使用免 费的动态域名将您的站点发布到互联网上。这时，您就需要像“花生壳”、“希网动态 ”域名这样的服务。对 于花生壳，您需要在本机安装它的linux动态域名客户端，对于“希网动态”你简单到只需要申请域名，然后采用 文本浏览器 lynx来获得动态域名客户端服务，方法是在终端命令行下键入：

lynx -mime_header -auth=用户名:用户名密码 "http://www.3322.org/dyndns/update?system=dyndns&hostname=您申请的域名 "。

至于端口映射，如果您使用的是ADSL，您需要路由功能将服务端口进行映射，很多ADSL拨号器都带有这样的功能。对于专门代拨号功能的路由器，其设置起 来更为简单。如果您是接入的公司或者其他类型的局域网，那么需要您和网络管理员联系。具体的方法，见各 种ADSL Modem及路由器的端口映射方法。

当然，你还可以采用其他内容管理系统来进行网站的安装发布，具体可以可以从OpenCMS了解。

11.跨 平台移植

   跨平台工具：Virtualbox， Easywine，CrossOveroffice和Hiweedlayer，可以安装运行来自windows的软件。
  EasyWine和CrossOver Office可以安装windows软件，而hiweedlayer则可以直接运行windows下的绿色软件。
 Virtualbox需要将用户自己加入到vboxusers组中才能正常运行，方法是直接编辑 /etc/group，用户名加入组中，用逗号分隔开即可，即vboxusers:x:1001:bioinfoserv,bioinfoserv。

值得说明的像Vmware和Qmenu之类的虚拟机可以进行完整操作系统的模拟，这与此处所提到的虚拟软件有一定差别。

12. 生物软件系列：bioinfoserv

  主要包含GUI、CommandLine和web应用的生物软件：
  GUI的软件， 主要是图形界面操作的生物软件，目前主要安装利用bioinfoserv软件仓库进行安装，如Jemboss, Staden等。
  CommandLine软件， 它不需要图形操作界面的，事实上在Jemboss中基本都包含了，不过这种方式可以更好地进行参数选择，从而更有利于控制程序的运行效率，如blast， clustw, QTLChart等，系统没有默认安装，不过安装十分容易，参看下面的“生 物软件的搜索与安装”。
  Web应用的软件， 主要是利用网络服务器apache/apache2和jsp, php, perl等脚本语言来支持运行的程序，使用的时候之需要打开浏览器，就可以轻松地使用软件，这种软件部署方式主要是为了利于程序的共享使用。其效率受网络 速度和程序编写的可靠性影响。本系统在/var/www/biotools下具有多个web应用软件，如InterproScan(jips)，wEMBOSS,phpPhyloTree, Sequence Manipulation Suite，这些均可直接从菜单打开，而且您还可以扩展web应用的生物软件， 方法是将web应用软件拷贝到这个目录，然后安装它们各自的安装和使用浏览器方式启动。

当然还有些生物软件应用充分地结合了浏览器，特别是firefox的插件。现在有较多的生物软件应用被写成了插件直接安装到firefox中，极大地方便 了使用者，如biobar, biofox和 zotero等。本系统浏览器已经安装好这些插件。
以下是相关生物软件的说明,没有具体翻译过来了,因为 有些语句实在翻译得不贴切,再说既然您是生物专业的使用者,这些英文理解起来也是小儿科了：
bioinfoserv-act - ACT (Artemis Comparison Tool) is a DNA sequence comparison viewer based on Artemis
bioinfoserv-ape - APE (Analyses of Phylogenetics and Evolution) is a package written in R. APE aims to be both a computing tool to analyse phylogenetic and evolutionary data, and an environment to develop and implement new analytical methods.
bioinfoserv-arb - The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis.
bioinfoserv-artemis - Artemis is a free genome viewer and annotation tool
bioinfoserv-base-directories - Initial bioinfoserv package which creates directories, installs configuration and support files for bioinfoserv.
bioinfoserv-big-blast - This script will chop up a large sequence, run blast on each bit and then write out an EMBL feature table and a MSPcrunch -d file containing the hits.
bioinfoserv-biojava - BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It include objects for manipulating sequences, file parsers, DAS client and server suport, access to BioSQL and Ensembl databases, and powerful analysis and statistical routines including a dynamic programming toolkit.
bioinfoserv-blast - BLAST 2.2.15, (Basic Local Alignment Search Tool), provides a method for rapid searching of nucleotide and protein databases.
bioinfoserv-bldp-files - bioinfoserv package providing organised searching facilities and access to bioinformatics software descriptions and documentation, including links to homepages, remote and local documentation. 
bioinfoserv-blixem - blixem, which stands for BLast matches In an X-windows Embedded Multiple alignment, is an interactive browser of pairwise Blast matches that have been stacked up in a master-slave multiple alignment.
bioinfoserv-cap3 - A base calling system.
bioinfoserv-clcworkbench - CLC Free Workbench is a graphical interface allowing the user to carry out many basic bioinformatics tasks.
bioinfoserv-clustal - Clustal X is a new windows interface for the ClustalW multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analysing the results.
bioinfoserv-coalesce - Fits the model which has a single population of constant size, and estimates 4Nu, where N is the effective population size and u is the neutral mutation rate per site.
bioinfoserv-documentation - Centralised documentation folder for bioinformatics software on bioinfoserv
bioinfoserv-dotter - Dotter is a graphical dotplot program for detailed comparison of two sequences.
bioinfoserv-dust - Dust - repetitive sequence masker
bioinfoserv-eclipse - Eclipse is a kind of universal tool platform - an open extensible IDE for anything and nothing in particular.
bioinfoserv-emboss - Emboss contains an extensive set of tools for bioinformatics and biological database management.
bioinfoserv-emboss-kmenus - Window manager menus and wrappers scripts for EMBOSS written by Thomas Siegmund (http://userpage.fu-berlin.de/~sgmd/)
bioinfoserv-envbase-for-pedro - This adds the necessary settings and template for Pedro to edit EnvBase files, including integration with TaxInspector and an icon for you to click.
bioinfoserv-estferret - ESTFerret processes, clusters and annotates EST data.
bioinfoserv-estscan - ESTScan is a program that can detect coding regions in DNA sequences, even if they are of low quality. It will also detect and correct sequencing errors that lead to frameshifts.
bioinfoserv-fastDNAml - fastDNAml is a program for estimating maximum likelihood phylogenetic trees from nucleotide sequences.
bioinfoserv-fasta - FASTA contains many programs for searching DNA and protein databases and for evaluating statistical significance from randomly shuffled sequences.
bioinfoserv-fluctuate - Fits the model which has a single population which has been growing (or shrinking) according to an exponential growth law.
bioinfoserv-forester - ATV (A Tree Viewer) is a Java tool for the visualization of annotated phylogenetic trees.
bioinfoserv-genquery - GenQuery is a set of Perl libraries for managing SQL query templates and making web-based query forms.
bioinfoserv-glimmer - Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.
bioinfoserv-gsrint - Scripts for use within GeneSpring
bioinfoserv-handlebar - Handlebar (previously known as BarcodeBase) is a database for storing data about barcodes and acessing the data via a web front-end.
bioinfoserv-happy - HAPPY: a software package for Multipoint QTL Mapping in Genetically Heterogeneous Animals
bioinfoserv-hmmer - HMMER is an implementation of profile HMM methods for sensitive database searches using multiple sequence alignments as queries.
bioinfoserv-jalview - Jalview is a Java multiple alignment editor
bioinfoserv-lamarc - Estimates population parameters using Likelihood Analysis using Random Coalescence.
bioinfoserv-lucy - Lucy is a utility that prepares raw DNA sequence fragments for sequence assembly, possibly using the TIGR Assembler. The cleanup process includes quality assessment, confidence reassurance, vector trimming and vector removal.
bioinfoserv-maxd - maxd is a data warehouse and visualisation environment for genomic expression data.
bioinfoserv-mcl - TribeMCL is a method for clustering proteins into related groups, which are termed 'protein families'. This clustering is achieved by analysing similarity patterns between proteins in a given dataset, and using these patterns to assign proteins into related groups. In many cases, proteins in the same protein familywill have similar functional properties. TribeMCL uses a novel clustering method (Markov Clustering or MCL) which solves problems which normally hinder protein sequence clustering. These problems include: multi-domain proteins, peptide fragments and proteins which possess domains which are very widespread (promiscuous domains). The efficiency of the method makes it applicable to the clustering of very large datasets.
bioinfoserv-mesquite - Mesquite is software for evolutionary , designed to help biologists analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis.
bioinfoserv-migrate - Estimates effective population sizes and past migration rates between n populations.
bioinfoserv-mountapp - Mountapp provides a small docked area for mounting filesystems
bioinfoserv-mrbayes - MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations.
bioinfoserv-mrbayes-multi - MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. This version has been compiled to run on multiple processors.
bioinfoserv-msatfinder - Microsatellite Finder
bioinfoserv-mspcrunch - MSPcrunch is a BLAST post-processing filter.
bioinfoserv-mummer - MUMmer is a system for rapidly aligning entire genomes.
bioinfoserv-muscle - A bioinfoserv wrapper for the muscle package maintained by Steffan Moeller.
bioinfoserv-mview - MView is a tool for converting the results of a sequence database search (BLAST, FASTA, etc.) into the form of a coloured multiple alignment of hits stacked against the query. Alternatively, an existing multiple alignment (MSF, PIR, CLUSTAL, etc.) can be processed.
bioinfoserv-netblast - NetBLAST searches for sequences similar to a query sequence. The query and the database searched can be either peptide or nucleic acid in any combination. NetBLAST can search only databases maintained at the National Center for Biotechnology Information (NCBI) in Bethesda, Maryland, USA.
bioinfoserv-njplot - NJPLOT is a phylogenetic tree drawing program that handles files describing trees by the nested parentheses method.
bioinfoserv-nrdb - nrdb can be used to generate quasi-nonredundant protein and nucleotide sequence databases.
bioinfoserv-ocount - Ocount - oligonucleotide frequency counter.
bioinfoserv-oligoarray - OligoArray 2.1 is free software that computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction.
bioinfoserv-oligoarrayaux - OligoArrayAux 2.1 is free software that is required for the OligoArray2.1 software.
bioinfoserv-omegamap - OmegaMap is a program for detecting natural selection and recombination in DNA or RNA sequences.
bioinfoserv-paml - PAML is a program package for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang.
bioinfoserv-partigene - PartiGene is used to cluster sequences and run initial blast searches for basic annotation purposes.
bioinfoserv-pedro - Pedro is an application that creates data entry forms based on a data model written in a particular style of XML Schema.
bioinfoserv-peptidemapper - PeptideMapper is a simple peptide mapping tool written by Rob Beynon, Protein Function Group, University of Liverpool. This presentation tool generates SVG files. The homepage for this package is: http://www.liv.ac.uk/pfg/Tools.html
bioinfoserv-pfaat - The Pfaat protein family alignment annotation tool is a Java-based multiple sequence alignment editor and viewer designed for protein family analysis. The application merges display features such as dendrograms, secondary and tertiary protein structures.
bioinfoserv-pftools - The 'pftools' package is a collection of experimental programs supporting the generalized profile format and search method of PROSITE.
bioinfoserv-phylip - PHYLIP is a free package of programs for inferring phylogenies. It is distributed as source code, documentation files, and a number of different types of executables.
bioinfoserv-prank - Prank is multiple alignment software as described in the paper "An algorithm for progressive multiple alignment of sequences with insertions" (PNAS 102:10557--10562). The author of the software is Ari Loytynoja (ari@ebi.ac.uk).
bioinfoserv-priam - Priam - a program to generate enzyme-specific profiles for metabolic pathyway prediction.
bioinfoserv-primer3 - Primer3 picks primers for PCR reactions.
bioinfoserv-prot4est - prot4EST is designed to translate error-prone nucleotide sequences producing robust polypeptide predictions.
bioinfoserv-qtlcart - QTL Cartographer is a suite of programs to map quantitative traits using a map of molecular markers.
bioinfoserv-rasmol - RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images.
bioinfoserv-rbs-finder - A program to find Ribosomal binding sites.
bioinfoserv-readseq - Read & reformat biosequences, Java command-line version.
bioinfoserv-recombine - Fits a model which has a single population of constant size with a single recombination rate across all sites.
bioinfoserv-sampledata - Sample data for bioinfoserv packages
bioinfoserv-seaview - SeaView is a graphical multiple sequence alignment editor developped by Manolo Gouy. SeaView is able to read and write various alignment formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to manually edit the alignment, and also to run DOT-PLOT or CLUSTALW programs to locally improve the alignment.
bioinfoserv-sequin - Sequin is a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank, EMBL, or DDBJ sequence databases.
bioinfoserv-splitstree - SplitsTree uses the split decomposition method to analyze and visualize distance data, especially extracted from biological sequences
bioinfoserv-staden - Staden is a suite of tools for bioinformatics analysis.
bioinfoserv-stars - STARS is an alternative interface to staden for studying polymorphisms in short sequences with batch processing, manual editing, trace viewing and data management. STARS was initially designed for Multi Locus Sequence Typing of bacteria.
bioinfoserv-t-coffee - T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Version 2.00 and higher can mix sequences and structures.
bioinfoserv-taverna - Taverna is a graphical client for setting up workflows that make use of web services.
bioinfoserv-taxinspector - TaxInspector is a browser for entries in the NCBI taxonomy database.
bioinfoserv-tetra - TETRA - tetranucleotide frequency calculator with GUI.
bioinfoserv-themes - Graphics, icons, KDE splash screen and a GDM theme for bioinfoserv.
bioinfoserv-trace2dbest - Processes trace files into dbEST submissions
bioinfoserv-transterm - Ocount - oligonucleotide frequency counter.
bioinfoserv-transterm-hp - Ocount - oligonucleotide frequency counter.
bioinfoserv-tree-puzzle - TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. It implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch.
bioinfoserv-treeview - TreeView is a simple program for displaying phylogenies.
bioinfoserv-trnascan - tRNAscan-SE searches for tRNA genes in genomic sequences.
bioinfoserv-wise2 - Wise2 is a package focused on comparisons of biopolymers, commonly DNA sequence and protein sequence.
bioinfoserv-yamap - Yet Another Microbial Annotation Pipeline.

13. 其他软件和应用环境

   网页制作：nvu
   文件比较：meld
   辞典 ：星际译王（这个词典目前安装了7部辞典，可以满足科技方面的释词，更多的词典库您可以自己编写或者下载安装。
   单词背诵 ：轻轻松松背单词（学英语单词很好的软件）
   软件安装卸载 ：synaptic，即新立得软件包管理器
   三维桌面：beryl+xgl，您还可以使用lg3d来 满足您的三维桌面需求，不过效果没有beryl＋xgl那么好。
   Java运 行环境：您可以安装 j2re1.4, j2sdk1.4, sun-java5, sun-java5-jdk, sun-java5-jre可以很好地满足其他需要java运行环境的软件需求。值得注意的是j2re1.4对汉字支持不很好（当然要配置它，您可以参 照，您可以使用sun- java5/6来代替。

BioInfoServ Project Team (c) 2008