https://e4d.pnnl.gov/Pages/Home.aspx 分布式内存并行处理软件包。 Pre-desiccation ERT image from the Hanford Site BC-Cribs desiccation treatability test Truex MJ, TC Johnson, CE Strickland, JE Peterson, and SS Hubbard. 2013. Monitoring Vadose Zone Desiccation with Geophysical Methods. Vadose Zone Journal 12(2):,doi:10.2136/vzj2012.0147 Surface Based ERT depth sections of conductivity beneath the Hanford Site BC-Cribs and Trenches ERT data courtesy hydroGEOPHYSICS Inc. E4D is a three-dimensional (3D) modeling and inversion code designed for subsurface imaging and monitoring using static and time-lapse 3D electrical resistivity (ER) or spectral induced polarization (SIP) data. To address the computational demands of inverting large scale 3D and 4D data sets, E4D was designed specifically to run on Linux/Unix-based distributed-memory, parallel, high-performance computing systems. However, E4D will run on any system with at least two processing cores, and can be compiled for Windows-based operating systems using Cygwin , ( see installation documentation-Section 3.0 ). E4D executes by reading a number of user-created ascii text input files, executing a particular run mode (e.g.; mesh generation, ER forward simulation, ER inversion, SIP inversion etc), and reporting results. Run-time options made available through input files are designed to enable flexibility and a high level of customization for a particular problem, making E4D suitable for both advanced research applications as well as more common imaging problems. See capabilities page for further information. A critical component of E4D is visualization. The E4D distribution includes the utility program bx, which places E4D simulation results into an exodus II finite-element, data-model-formatted file. Exodus II files are then visualized using the VisIt visualization program, an open-source visualization code developed by the Lawrence Livermore National Laboratory. Although E4D documentation focuses on the use of VisIt, all of the files necessary for users to develop and operate other visualization codes are provided by E4D. Guidance concerning the use of VisIt is provided on the VisIt website, and is not provided with the E4D user documentation The intended audience for E4D includes researchers and other practitioners familiar with electrical geophysical methods and deterministic geophysical inversion. This website provides information concerning capabilities , availability and licensing , download and installation , and quality assurance testing and documentation . Guidance concerning the use of E4D is provided in the E4D Users Guide , which is included with the E4D distribution. Capabilities Mesh Generation E4D computes the subsurface potential distribution arising from a known current source using the weak form finite element solution to the Poison equation on an unstructured tetrahedral mesh. Mesh generation capabilities are provided by the 2D triangular mesh generator Triangle , and the 3D tetrahedral mesh generator TetGen . E4D constructs the input files for Triangle and TetGen b ased on a user generated mesh configuration file to produce a customized tetrahedral mesh. The interface provided by E4D enabl es efficient modeling of surface topography subsurface features with known location and dimension (i.e. geologic boundaries, wellbores, buried tanks and pipes, water table boundaries, non-point electrodes etc.). These features can be used to constrain the inverse problem using a flexible set of conditional imaging constraints based the method of Iteratively Reweighted Least Squares, thereby enabling users to incorporate known information into the inversion problem to improve imaging resolution. Computational mesh visualization for E4D tutorial 1.2. Forward Modeling Forward modeling is referred to herein as the process whereby E4D simulates the subsurface potential distribution arising from a current injection event, and/or to the process whereby E4D simulates an Electrical Resistivity Tomography or Spectral Induced Polarization survey. Forward modeling is a critical component of the imaging algorithm, and is also essential for assessing the performance of a given electrode configuration and measurement sequence under likely field conditions. E4D was designed to facilitate forward modeling studies by enabling visualization of potential distributions (both real and complex), by generating the files by which to compare simulated data with observed data, and by simulating ERT and SIP surveys. When executed in forward modes, E4D automatically generates the survey files necessary to invert the synthetic data in order to investigate, for example, the influence of electrode placement, measurement sequence, model constraints, mesh refinement, and data noise on imaging resolution. E4D also computes the analytic ERT solution for a homogeneous half-space, which facilitates analysis of numeric solution accuracy for a given mesh refinement. Forward modeling examples are provided and used extensively in the tutorial sections of the E4D User Guide contained at the end of each chapter. Complex potential simulation visualization and corresponding error analysis. Inversion Constraints E4D is implemented with a flexible set of tools enabling users to supply the inversion with prior information. These tools include customized mesh capabilities, which enable users to place known boundaries in the mesh, and to use those boundaries to formulate constraints on the inversion. The constraints themselves are user chosen according to one or more structural metrics coupled with a corresponding weighting function, and are applied using the method of Iteratively Reweighted Least Squares. The weighting functions determine the conditions under which the structural metrics (e.g. similarity constraints, inequality constraints, known value constraints etc.) should be applied to the inversion. Constraint settings can be adjusted to inform the inversion of numerous conditions, for example, the upper and lower conductivity limits of a particular mesh zone, the sign of the change in conductivity across a known boundary or time, the conductivity gradient at which a similarity constraint should be removed, or the conductivity values that the inversion is allowed to use to fit the data (i.e. a piecewise constant inversion). Some examples of these capabilities are provided in the tutorial sections of the E4D User Guide . Details concerning the inverse solution constraint capabilities implemented in E4D are provided in the E4D Theory Guide. Bulk conductivity distribution beneath vadose zone waste infiltration galleries at the the Hanford Site B-Complex near Richland WA, USA.
Integrated solutions * CLCbio Genomics Workbench - de novo and reference assembly of Sanger, Roche FLX, Illumina, Helicos, and SOLiD data. Commercial next-gen-seq software that extends the CLCbio Main Workbench software. Includes SNP detection, CHiP-seq, browser and other features. Commercial. Windows, Mac OS X and Linux. * Galaxy - Galaxy = interactive and reproducible genomics. A job webportal. * Genomatix - Integrated Solutions for Next Generation Sequencing data analysis. * JMP Genomics - Next gen visualization and statistics tool from SAS. They are working with NCGR to refine this tool and produce others. * NextGENe - de novo and reference assembly of Illumina, SOLiD and Roche FLX data. Uses a novel Condensation Assembly Tool approach where reads are joined via anchors into mini-contigs before assembly. Includes SNP detection, CHiP-seq, browser and other features. Commercial. Win or MacOS. * SeqMan Genome Analyser - Software for Next Generation sequence assembly of Illumina, Roche FLX and Sanger data integrating with Lasergene Sequence Analysis software for additional analysis and visualization capabilities. Can use a hybrid templated/de novo approach. Commercial. Win or Mac OS X. * SHORE - SHORE, for Short Read, is a mapping and analysis pipeline for short DNA sequences produced on a Illumina Genome Analyzer. A suite created by the 1001 Genomes project. Source for POSIX. * SlimSearch - Fledgling commercial product. Align/Assemble to a reference * BFAST - Blat-like Fast Accurate Search Tool. Written by Nils Homer, Stanley F. Nelson and Barry Merriman at UCLA. * Bowtie - Ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of 25 million reads per hour on a typical workstation with 2 gigabytes of memory. Uses a Burrows-Wheeler-Transformed (BWT) index. Link to discussion thread here . Written by Ben Langmead and Cole Trapnell. Linux, Windows, and Mac OS X. * BWA - Heng Lee's BWT Alignment program - a progression from Maq. BWA is a fast light-weighted tool that aligns short sequences to a sequence database, such as the human reference genome. By default, BWA finds an alignment within edit distance 2 to the query sequence. C++ source. * ELAND - Efficient Large-Scale Alignment of Nucleotide Databases. Whole genome alignments to a reference genome. Written by Illumina author Anthony J. Cox for the Solexa 1G machine. * Exonerate - Various forms of pairwise alignment (including Smith-Waterman-Gotoh) of DNA/protein against a reference. Authors are Guy St C Slater and Ewan Birney from EMBL. C for POSIX. * GenomeMapper - GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. A tool created by the 1001 Genomes project. Source for POSIX. * GMAP - GMAP (Genomic Mapping and Alignment Program) for mRNA and EST Sequences. Developed by Thomas Wu and Colin Watanabe at Genentec. C/Perl for Unix. * gnumap - The Genomic Next-generation Universal MAPper (gnumap) is a program designed to accurately map sequence data obtained from next-generation sequencing machines (specifically that of Solexa/Illumina) back to a genome of any size. It seeks to align reads from nonunique repeats using statistics. From authors at Brigham Young University. C source/Unix. * MAQ - Mapping and Assembly with Qualities (renamed from MAPASS2). Particularly designed for Illumina with preliminary functions to handle ABI SOLiD data. Written by Heng Li from the Sanger Centre. Features extensive supporting tools for DIP/SNP detection, etc. C++ source * MOSAIK - MOSAIK produces gapped alignments using the Smith-Waterman algorithm. Features a number of support tools. Support for Roche FLX, Illumina, SOLiD, and Helicos. Written by Michael Str?mberg at Boston College. Win/Linux/MacOSX * MrFAST and MrsFAST - mrFAST mrsFAST are designed to map short reads generated with the Illumina platform to reference genome assemblies; in a fast and memory-efficient manner. Robust to INDELs and MrsFAST has a bisulphite mode. Authors are from the University of Washington. C as source. * MUMmer - MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. Released as a package providing an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools. Version 3.0 was developed by Stefan Kurtz, Adam Phillippy, Arthur L Delcher, Michael Smoot, Martin Shumway, Corina Antonescu and Steven L Salzberg - most of whom are at The Institute for Genomic Research in Maryland, USA. POSIX OS required. * Novocraft - Tools for reference alignment of paired-end and single-end Illumina reads. Uses a Needleman-Wunsch algorithm. Can support Bis-Seq. Commercial. Available free for evaluation, educational use and for use on open not-for-profit projects. Requires Linux or Mac OS X. * PASS - It supports Illumina, SOLiD and Roche-FLX data formats and allows the user to modulate very finely the sensitivity of the alignments. Spaced seed intial filter, then NW dynamic algorithm to a SW(like) local alignment. Authors are from CRIBI in Italy. Win/Linux. * RMAP - Assembles 20 - 64 bp Illumina reads to a FASTA reference genome. By Andrew D. Smith and Zhenyu Xuan at CSHL. (published in BMC Bioinformatics). POSIX OS required. * SeqMap - Supports up to 5 or more bp mismatches/INDELs. Highly tunable. Written by Hui Jiang from the Wong lab at Stanford. Builds available for most OS's. * SHRiMP - Assembles to a reference sequence. Developed with Applied Biosystem's colourspace genomic representation in mind. Authors are Michael Brudno and Stephen Rumble at the University of Toronto. POSIX. * Slider - An application for the Illumina Sequence Analyzer output that uses the probability files instead of the sequence files as an input for alignment to a reference sequence or a set of reference sequences. Authors are from BCGSC. Paper is here . * SOAP - SOAP (Short Oligonucleotide Alignment Program). A program for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. The updated version uses a BWT. Can call SNPs and INDELs. Author is Ruiqiang Li at the Beijing Genomics Institute. C++, POSIX. * SSAHA - SSAHA (Sequence Search and Alignment by Hashing Algorithm) is a tool for rapidly finding near exact matches in DNA or protein databases using a hash table. Developed at the Sanger Centre by Zemin Ning, Anthony Cox and James Mullikin. C++ for Linux/Alpha. * SOCS - Aligns SOLiD data. SOCS is built on an iterative variation of the Rabin-Karp string search algorithm, which uses hashing to reduce the set of possible matches, drastically increasing search speed. Authors are Ondov B, Varadarajan A, Passalacqua KD and Bergman NH. * SWIFT - The SWIFT suit is a software collection for fast index-based sequence comparison. It contains: SWIFT — fast local alignment search, guaranteeing to find epsilon-matches between two sequences. SWIFT BALSAM — a very fast program to find semiglobal non-gapped alignments based on k-mer seeds. Authors are Kim Rasmussen (SWIFT) and Wolfgang Gerlach (SWIFT BALSAM) * SXOligoSearch - SXOligoSearch is a commercial platform offered by the Malaysian based Synamatix . Will align Illumina reads against a range of Refseq RNA or NCBI genome builds for a number of organisms. Web Portal. OS independent. * Vmatch - A versatile software tool for efficiently solving large scale sequence matching tasks. Vmatch subsumes the software tool REPuter, but is much more general, with a very flexible user interface, and improved space and time requirements. Essentially a large string matching toolbox. POSIX. * Zoom - ZOOM (Zillions Of Oligos Mapped) is designed to map millions of short reads, emerged by next-generation sequencing technology, back to the reference genomes, and carry out post-analysis. ZOOM is developed to be highly accurate, flexible, and user-friendly with speed being a critical priority. Commercial. Supports Illumina and SOLiD data. De novo Align/Assemble * ABySS - Assembly By Short Sequences. ABySS is a de novo sequence assembler that is designed for very short reads. The single-processor version is useful for assembling genomes up to 40-50 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes. By Simpson JT and others at the Canada's Michael Smith Genome Sciences Centre. C++ as source. * ALLPATHS - ALLPATHS: De novo assembly of whole-genome shotgun microreads. ALLPATHS is a whole genome shotgun assembler that can generate high quality assemblies from short reads. Assemblies are presented in a graph form that retains ambiguities, such as those arising from polymorphism, thereby providing information that has been absent from previous genome assemblies. Broad Institute. * Edena - Edena (Exact DE Novo Assembler) is an assembler dedicated to process the millions of very short reads produced by the Illumina Genome Analyzer. Edena is based on the traditional overlap layout paradigm. By D. Hernandez, P. Fran?ois, L. Farinelli, M. Osteras, and J. Schrenzel. Linux/Win. * EULER-SR - Short read de novo assembly. By Mark J. Chaisson and Pavel A. Pevzner from UCSD (published in Genome Research). Uses a de Bruijn graph approach. * MIRA2 - MIRA (Mimicking Intelligent Read Assembly) is able to perform true hybrid de-novo assemblies using reads gathered through 454 sequencing technology (GS20 or GS FLX). Compatible with 454, Solexa and Sanger data. Linux OS required. * SEQAN - A Consistency-based Consensus Algorithm for De Novo and Reference-guided Sequence Assembly of Short Reads. By Tobias Rausch and others. C++, Linux/Win. * SHARCGS - De novo assembly of short reads. Authors are Dohm JC, Lottaz C, Borodina T and Himmelbauer H. from the Max-Planck-Institute for Molecular Genetics. * SSAKE - The Short Sequence Assembly by K-mer search and 3' read Extension (SSAKE) is a genomics application for aggressively assembling millions of short nucleotide sequences by progressively searching for perfect 3'-most k-mers using a DNA prefix tree. Authors are René Warren, Granger Sutton, Steven Jones and Robert Holt from the Canada's Michael Smith Genome Sciences Centre. Perl/Linux. * SOAPdenovo - Part of the SOAP suite. See above. * VCAKE - De novo assembly of short reads with robust error correction. An improvement on early versions of SSAKE. * Velvet - Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454. Need about 20-25X coverage and paired reads. Developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI). SNP/Indel Discovery * ssahaSNP - ssahaSNP is a polymorphism detection tool. It detects homozygous SNPs and indels by aligning shotgun reads to the finished genome sequence. Highly repetitive elements are filtered out by ignoring those kmer words with high occurrence numbers. More tuned for ABI Sanger reads. Developers are Adam Spargo and Zemin Ning from the Sanger Centre. Compaq Alpha, Linux-64, Linux-32, Solaris and Mac * PolyBayesShort - A re-incarnation of the PolyBayes SNP discovery tool developed by Gabor Marth at Washington University. This version is specifically optimized for the analysis of large numbers (millions) of high-throughput next-generation sequencer reads, aligned to whole chromosomes of model organism or mammalian genomes. Developers at Boston College. Linux-64 and Linux-32. * PyroBayes - PyroBayes is a novel base caller for pyrosequences from the 454 Life Sciences sequencing machines. It was designed to assign more accurate base quality estimates to the 454 pyrosequences. Developers at Boston College. Genome Annotation/Genome Browser/Alignment Viewer/Assembly Database * EagleView - An information-rich genome assembler viewer. EagleView can display a dozen different types of information including base quality and flowgram signal. Developers at Boston College. * LookSeq - LookSeq is a web-based application for alignment visualization, browsing and analysis of genome sequence data. LookSeq supports multiple sequencing technologies, alignment sources, and viewing modes; low or high-depth read pileups; and easy visualization of putative single nucleotide and structural variation. From the Sanger Centre. * MapView - MapView: visualization of short reads alignment on desktop computer. From the Evolutionary Genomics Lab at Sun-Yat Sen University, China. Linux. * SAM - Sequence Assembly Manager. Whole Genome Assembly (WGA) Management and Visualization Tool. It provides a generic platform for manipulating, analyzing and viewing WGA data, regardless of input type. Developers are Rene Warren, Yaron Butterfield, Asim Siddiqui and Steven Jones at Canada's Michael Smith Genome Sciences Centre. MySQL backend and Perl-CGI web-based frontend/Linux. * STADEN - Includes GAP4. GAP5 once completed will handle next-gen sequencing data. A partially implemented test version is available here * XMatchView - A visual tool for analyzing cross_match alignments. Developed by Rene Warren and Steven Jones at Canada's Michael Smith Genome Sciences Centre. Python/Win or Linux. Counting e.g. CHiP-Seq, Bis-Seq, CNV-Seq * BS-Seq - The source code and data for the Shotgun Bisulphite Sequencing of the Arabidopsis Genome Reveals DNA Methylation Patterning Nature paper by Cokus et al. (Steve Jacobsen's lab at UCLA). POSIX. * CHiPSeq - Program used by Johnson et al. (2007) in their Science publication * CNV-Seq - CNV-seq, a new method to detect copy number variation using high-throughput sequencing. Chao Xie and Martti T Tammi at the National University of Singapore. Perl/R. * FindPeaks - perform analysis of ChIP-Seq experiments. It uses a naive algorithm for identifying regions of high coverage, which represent Chromatin Immunoprecipitation enrichment of sequence fragments, indicating the location of a bound protein of interest. Original algorithm by Matthew Bainbridge, in collaboration with Gordon Robertson. Current code and implementation by Anthony Fejes. Authors are from the Canada's Michael Smith Genome Sciences Centre. JAVA/OS independent. Latest versions available as part of the Vancouver Short Read Analysis Package * MACS - Model-based Analysis for ChIP-Seq. MACS empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size estimates, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome sequence, allowing for more sensitive and robust prediction. Written by Yong Zhang and Tao Liu from Xiaole Shirley Liu's Lab. * PeakSeq - PeakSeq: Systematic Scoring of ChIP-Seq Experiments Relative to Controls. a two-pass approach for scoring ChIP-Seq data relative to controls. The first pass identifies putative binding sites and compensates for variation in the mappability of sequences across the genome. The second pass filters out sites that are not significantly enriched compared to the normalized input DNA and computes a precise enrichment and significance. By Rozowsky J et al. C/Perl. * QuEST - Quantitative Enrichment of Sequence Tags. Sidow and Myers Labs at Stanford. From the 2008 publication Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data . (C++) * SISSRs - Site Identification from Short Sequence Reads. BED file input. Raja Jothi @ NIH. Perl. **See also this thread for ChIP-Seq, until I get time to update this list. Alternate Base Calling * Rolexa - R-based framework for base calling of Solexa data. Project publication * Alta-cyclic - a novel Illumina Genome-Analyzer (Solexa) base caller Transcriptomics * ERANGE - Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq. Supports Bowtie, BLAT and ELAND. From the Wold lab. * G-Mo.R-Se - G-Mo.R-Se is a method aimed at using RNA-Seq short reads to build de novo gene models. First, candidate exons are built directly from the positions of the reads mapped on the genome (without any ab initio assembly of the reads), and all the possible splice junctions between those exons are tested against unmapped reads. From CNS in France. * MapNext - MapNext: A software tool for spliced and unspliced alignments and SNP detection of short sequence reads. From the Evolutionary Genomics Lab at Sun-Yat Sen University, China. * QPalma - Optimal Spliced Alignments of Short Sequence Reads. Authors are Fabio De Bona, Stephan Ossowski, Korbinian Schneeberger, and Gunnar R?tsch. A paper is available . * RSAT - RSAT: RNA-Seq Analysis Tools. RNASAT is developed and maintained by Hui Jiang at Stanford University. * TopHat - TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. TopHat is a collaborative effort between the University of Maryland and the University of California, Berkeley 转载自： http://blog.163.com/luyiming_1986@126/blog/static/151141532201122494757719/ 二代测序数据预处理与分析 常使用的工具列表 质量控制Quality Control：FastQC、Fastx-toolkit 拼接Aligner：BWA，Bowtie, Tophat, SOAP2 Mapper：Tophat, Cufflinks 基因定量 Gene Quantification: Cufflinks, Avadis NGS 质量改进 Quality improvement: Genome Analysis Toolkit(GATK) SNP: Unified Genotyper,Glfmultiple, SAMtools, Avadis NGS CNV: CNVnator Indel: Pindel, Dindel, Unified Genotyper, Avadis NGS Mapping to a gene: Cufflinks, Rsamtools, Genomic Features 相关的数据格式 FASTQ: SAM: A generic nucleotide alignment format BAM: binary format VCF 数据处理的流程
包括多个应用程序： SeqBuilder - for sequence editing and annotation, automated virtual cloning, and primer design SeqMan Pro - for contig assembly and analysis, including SNP discovery, coverage evaluation, and project annotation MegAlign - for DNA and protein sequence alignments and analysis GeneQuest - for gene discovery and annotation Protean - for protein structure analysis and prediction PrimerSelect - for primer design EditSeq - for importing and editing unusual file types 链接： http://www.dnastar.com/t-sub-products-lasergene-seqmanpro.aspx
FindCrypt2是个功能强大的IDA插件，是FindCrypt的第二版，支持小端和大端格式(works with both little and big endian programs. It knows to reuse old slots in the bookmarks if run repeatedly. It is fully automatic and scans each new created database. Manual scan is still available.). 从网上下载到的IDA5.1包是个功能齐全的软件包。包括了SDK等重要部分（未包括 hex-rays Decompiler）。 从网上可以下载到FindCrypt2包，有些会包含编译好的findcrypt.plw，只需拷贝到IDA的plugins目录即可。 若未包含findcrypt.plw，或者版本不符，可以使用IDASDK对FindCrypt2的源码进行编译，生成findcrypt.plw。 我下载的 这个包中 已经包含findcrypt.plw，放到IDA5.1的plugins目录，启动并打开一个exe文件，在分析阶段就已经看到了FindCrypt2的分析结果。也可以通过Edit Plugins Find Crypt v2 执行。 ---------------------------------------------------------------------------------------------- File 'C:\Program Files\FoxitReader\Foxit Reader.exe' is successfully loaded into the database. 4B18DD: found sparse constants for SHA-1 4B2FAD: found sparse constants for MD4 4B30C0: found sparse constants for MD5 53A69C: found sparse constants for MD4 53A8E9: found sparse constants for MD5 86E584: found const array Rijndael_Te0 (used in Rijndael) 86E984: found const array Rijndael_Te1 (used in Rijndael) 86ED84: found const array Rijndael_Te2 (used in Rijndael) 86F184: found const array Rijndael_Te3 (used in Rijndael) 86F584: found const array Rijndael_Td0 (used in Rijndael) 86F984: found const array Rijndael_Td1 (used in Rijndael) 86FD84: found const array Rijndael_Td2 (used in Rijndael) 870184: found const array Rijndael_Td3 (used in Rijndael) 870598: found const array PKCS_DigestDecoration_MD2 (used in PKCS_MD2) 8705B0: found const array PKCS_DigestDecoration_MD5 (used in PKCS_MD5) 87B534: found const array Rijndael_Te0 (used in Rijndael) 87B934: found const array Rijndael_Te1 (used in Rijndael) 87BD34: found const array Rijndael_Te2 (used in Rijndael) 87C134: found const array Rijndael_Te3 (used in Rijndael) 87C534: found const array Rijndael_Td0 (used in Rijndael) 87C934: found const array Rijndael_Td1 (used in Rijndael) 87CD34: found const array Rijndael_Td2 (used in Rijndael) 87D134: found const array Rijndael_Td3 (used in Rijndael) 8C72E0: found const array zinflate_lengthExtraBits (used in zlib) 8C7354: found const array zinflate_distanceExtraBits (used in zlib) 94C850: found const array CRC32_m_tab (used in CRC32) Found 26 known constant arrays in total. ---------------------------------------------------------------------------------------------- 双击输出窗口中的输出行中的地址，即可在代码窗口转到相应的代码。 PS：今早（5.19）在IDA6.1上试了一下FindCrypt2也可以运行。
以下软件包含在两个 RAR 文件中，请下载后，解压安装。运行时会产生注册文件，一般是 registerinfo*.dat, 请将其发到 yjzhang@semi.ac.cn ， 张冶金，试用期为两周到四周，手机 13661385034 。 下载地址 http://www.oedcad.com/index.htm 如不能下载，请与 yjzhang@semi.ac.cn 联系。 光电子 、 光波、光通信仿真系列软件介绍 目前该软件包光子学模块已经被美国 MIT ，加州理工，斯坦福大学，英国卢瑟福实验室，澳大利亚，加拿大，伊朗，伊拉克，比利时，巴基斯坦，日本，新加坡及国内清华大学，北京大学，中科院，北京交通大学，上海交通大学，国防科技大学，武汉邮电学院，烽火等 50 个单位 300 多个用户使用。 用户可根据需要，输入关键字，搜索所需要功能模块，如想计算多层膜反射谱，可在面板搜索处，输入 “reflection spectrum”, 最右侧一栏会出现对应的 强大的光子光电子器件编辑模块 编辑模块支持一维二维及三维的全方位可视化编辑，包括各种复杂阵列，复杂图形，如各种光子晶体结构，表面等离子体，超导体，光子晶体光纤光栅及其拉伸渐变结构，各类量子阱，超晶格，超材料，左手材料等。介质支持量子阱超晶格及体材料等半导体有源介质，各向异性电磁介质，损耗介质，各种色散介质， kerr 及 raman 非线性介质，金属，等离子体介质，复介电系数介质等。支持自定义函数对结构及介质进行变化。支持图片输入，图片可以来自 TEM ， SEM 及 ATM ，也可以来自手工画制。 光子学仿真系统 对于光子结构及器件分析引入多种方法可以对光子能带，色散关系，态密度，群速度，传输特性，各种光栅透反射特性，模式特性，远场特性，近场特性，光纤泄漏损耗，模式面积，非线性因子，弯曲损耗，对接损耗，低阶及高阶色散，群时延，数值孔径， V 参数，耦合特性，放大特性，太阳能电池 VI 特性及效率，模式体积， Q 因子进行精确求解。支持大规模并行机群仿真。支持各种参数优化设计。其中包括方法有全矢量时域有限差分（ FDTD ），频域有限差分（ FDFD ），传递矩阵（ TMM ），散射矩阵（ SMM ），全矢量半矢量束传播（ BPM ），快速多极化（ MPM ），平面波展开法（ PWE ），有限元（ FEM ）等。可以使用户从不同角度利用不同方法对目标进行对比和分析，进行大规模拓扑优化。 1. 并行时域有限差分分析包 (PCFDTD) (Parallel cluster finite difference in time domain) 随着微电子集成度按照摩尔定律接近物理极限，光子集成被人们寄予厚望。 而仿真设计非常重要，对于光子器件而言，设计和仿真方法有很多种，但最后都需要通过 FDTD 来验证。对于大型器件或集成光路往往需要几十上百个 CPU 来进行并行高速处理。 PCFDTD 正是基于该应用而进行开发的。另外考虑到许多实验室二次开发的需要，我们将提供一些代码或开放接口，以便以此为基础，方便实验室进行有自己特色软件的开发。 PCFDTD 针对一维、二维及三维光子波导或器件进行 FDTD 的设计，支持损耗色散、非线性 , 各向异性及有源介质等 . 能够进行图片识别， 可以从实验获得的 SEM 图片或从其它渠道获得各种格式图片进行识别，直接导入结构，实现结构的精确测量，如占空比测试，可以对实验获得结构直接进行仿真，输出器件模式特性，传输特性。 支持有源器件 FDTD 仿真，如激光器， SOA 等。 支持单双精度运算。 支持无限次连续运算。 给出任意监测面的近场、远场分布，计算出远场发散角。 计算模式体积。 可以进行 PADE 非线性信号处理，能使对三维结构 Q 值计算加快 10 倍。下图为一典型 WG 模腔结构，该结构 Q 值可以达几十万甚至上百万，用普通方法计算 Q 值很困难，通过我们的 Pade 近似方法就能大幅度提高速度。 支持 FFT ， DFT ， FDM 等多种信号处理方法。 拓扑优化 拓扑优化常用于波导器件，如弯折处的计算， PCFDTD 可以对任意分布进行优化。下面举例说明。 如下图所示弯折波导，平面波源，水平监测点，可以监测功率等各种参数。 支持有源器件的瞬态特性仿真： 以上是对光子晶体 SOA 的 FDTD 分析，很得到其慢光延迟特性。 2. 多维传递矩阵分析包 (TMM) 传递矩阵法可以用来计算各种介质材料及金属材料的能带结构，能够进行二维及三维的能带计算及透反射特性计算。对于一些复杂的材料均可进行计算，适于对太阳能电池的效率进行分析。 3. 光子集成束传播分析包 (Beam Propagation Analysis System) 束传播方法是光子集成设计当中比较经典实用的方法，我们的 BPM 软件包括二维及三维标量、半矢量及矢量分析模块，可以支持多种输入方式。支持到 4 阶 PADE 算法及双向高速束传播。 支持损耗介质等。 4.N order 法能带及传输计算 能带计算包括金属等介质的能带结构及传输谱，输出特定 k 点的光场分布，群速度，状态密度等。 可以分析各种光子晶体 TE ， TM, 混合模式带结构，缺陷态，色散等特性。 能够进行二维及三维计算，与 TMM 模块， PWE 模块形成互补验证。 5. 光子晶体光纤及光波导模式分析包（ PCF CAD ） 光子晶体光纤的数值计算方法主要有：有效折射率法、平面波展开法、局域函数法、有限元法、时域有限差分法 (FDTD) ，多极化方法。这些方法各有千秋，例如有效折射率法要求芯区折射率大于包层的有效折射率，而且没法给出光纤的色散特性和偏振特性。时域有限差分法能适合各种截面但是计算量巨大。平面波展开法是比较常用的一种方法，它的基本思想是：将电磁场以平面波的形式展开，可以将麦克斯韦方程组化成一个本征方程组，求解该方程的本征值便得到传播的光子的本征频率。这种方法的不足之处是当光子晶体结构复杂或处理有缺陷的体系时，可能因为计算能力的限制而不能计算或者难以准确计算。而且如果介电常数不是常数而是随频率变化，就没有一个确定的本征方程形式，这种情况下根本无法求解。有限元法则具有灵活性和通用性，但是其计算的工作量惊人，原始数据复杂，而且边界条件复杂。 FDTD 则多用于求解传输问题。频域有限差分可以求解模式问题，但其与剖分点数及边界条件有很大关系关。多极化方法的好处在于它可以严格求解 Maxwell 方程，可以处理位置分布任意，具有任意折射率的孔，并且它可以给出色散曲线和偏振特性，而且计算量远小于 FDTD 。但是它也有不利之处就是难以处理非圆孔，但是由于光纤的制造技术，在光子晶体光纤中绝大多数都是圆孔，所以这个问题并不大。 本软件专门针对二维光子晶体或波导的设计，能够分析多种阵列结构。其中包括多极化方法，频域有限差分，时域有限差分，平面波展开法 , 矩阵法 , 束传播，有限元法等。可以计算场分布，有效折射率，有效面积，色散， NA ， bend loss,GAMA factor,splice loss, V parameter 等 . 6. 严格耦合波分析包 RCWA(Rigorous Couple Wave Analysis) 严格耦合波又称模式匹配法，是分析闪耀光栅、金属光栅的理想方法。该模块可以进行一维、二维及三维各种类型光栅分析，结果精确，能够进行高级数分析。由于我们采用了稳定算法及快速特征值求解技术，该模块与其它商业软件相比，速度更快，是其它软件的 5 倍左右。 7. 光纤光栅分析包（ OPTICAL GRATING ） 光栅是光通信中非常重要的器件，可以做色度色散补偿器，偏振模色散补偿器，可调色散补偿器，各种宽带窄带滤波器，梳状滤波器，光延迟线。光通信中的 DFB ， DBR 激光器等也是以光栅为核心的。光栅的设计尤其重要 。 OPTICAL GRATING 是以耦合波方程为基础的光栅设计模块，包括均匀，相移，采样，啁啾光栅的设计，能够进行各种函数的切趾仿真，还可以进行各种直流和交流调制。最后输出透射谱、反射谱及时延谱。然后形成光栅制作文件，用以驱动紫外曝光系统，形成光栅。该仿真系统是清华大学研究人员历经十几年的理论和实验工作研制出来的，利用该系统已经进行了超过 6000 小时的实验，完成上千万的国家任务。 8. 高速光通信系统分析包（ OFC CAD ） （ Optical Fiber Communication Analysis System ） 光纤通信系统仿真模块（ OFCCAD ）包括了近 70 种器件模型，包括各种激光器， EDFA 放大器， RAMAN 放大器，半导体放大器，波长变化器，各种码型发生器，光电脉冲调制器， EA 、位相、啁啾、频率调制器，光纤，光纤光栅，各种光电滤波器， PIN 、 APD 接收器， Sagnac 环，复用解复用器， Add/Drop ，光子晶体及光波导类器件，眼图、误码、频谱及信号监测器，环路控制，复合器件及开放式接口模块等，特点如下： 1. 把整个光纤通信系统分为发射部分，传输部分，接收部分和放大部分这四个子模块。针对光通信器件的未来发展趋势，加入了光子晶体器件设计的理论模型。该仿真系统的特色在于具有系统级和器件级仿真的双重功能，使得开发的新器件可在系统的框架下得到测试和应用。 2. 具有灵活易于扩展的自定义端口，多信道传输，重复单元传输， 复合模块传输的软件框架及数据结构，利用开放式接口，用户可以任 意加入设计代码，自行开发新型器件。 3. 具有完善的半导体异质结，量子阱等激光器的系统级和器件级 仿真模型，器件级模型包括一维，二维及三维的各种材料体系和结构 类型，并具有优化设计功能。 4. 完善的光纤光栅系统级及器件级模型，可模拟等周期，啁啾，相移，取样等各种光纤光栅，并支持多种切趾和线性及非线性采样。可以仿真各种光纤光栅级联，输出透射、反射及时延谱，并可在单信道，多信道及其它系统中进行模拟应用测试。 5. 包括 Sagnac 环器件级模型。 9. 平面展开法光子能带计算 PWE (Plane wave extension method) 平面波展开法 平面波展开法是分析周期结构，如光子晶体的能带结构标准方法。是一种在频域利用周期边界条件求解麦克斯维方程的方法，特点是精确，速度快。但是不能处理损耗、色散的介质。 PWE 模块采用 MIT 的 PBG linux 内核，设计了 windows 版本，使之更加实用化，可以分析一维，二维及三维结构的能带结构，输出特定 k 点的光场分布，群速度，状态密度等。 可以分析各种光子晶体 TE ， TM, 混合模式带结构，缺陷态，色散等特性。 The module is designed according to plane wave extension method, and you can see the reference: Block-iterative frequency-domain methods for Maxwell's equations in a planewave basis Steven G. Johnson and J. D. Joannopoulos Dept. of Physics and Center for Materials Science and Engineering,Massachusetts Institute of Technology, Cambridge, MA 02139 USA stevenj@alum.mit.edu http://ab-initio.mit.edu/ 29 January 2001 / Vol. 8, No. 3 / OPTICS EXPRESS 173 2. S. G. Johnson and J. D. Joannopoulos, The MIT Photonic-Bands Package home page http://ab-initio.mit.edu/mpb/ . 10. 掺铒光纤放大器分析包 EDFA Design System EDFA(Er doping fiber amplifier) is a famous device in optical fiber communication. In a WDM system, how to install EDFAs is important, which affects the flat of channel energy. This software dose it. You can obtain input and output spectrum, noise figure, and so on. EDFA 模块理论基础是 EDFA giles 模型，对于实际 EDFA 光纤，需要知道光纤的 giles 参数，该参数系统本身有缺省值，用户也可以自己提供，由上图的“增益损耗文件”处指定，这些参数是频率的函数，一般给定的范围是 C 波段，在“ system use ” 中，需要给定 980nm 和 1480nm 两个泵浦波长处的 giles 参数。每个 EDFA 最多可设 4 个泵浦，分别是前向 980nm,1480nm 泵源，后向 980nm,1480nm 泵源。可按用户需要设置任意信号光频率和平均功率，用户可用此事先检测放大特性，然后再进行系统传输，系统传输时将只利用泵浦参数，信号参数将针对模块入口所得到的。系统 ASE 噪声在每级放大之后将以高斯白噪声形式加到信号中，最多可进行四级放大。可通过 view test 按钮查看，增益谱情况及信号增益及噪声指数。 11. 拉曼放大器分析包 Raman Amplifier Design System Raman fiber amplifier is a new device in optical fiber communication. In a WDM system, how to configure RA is important, which affects the flat of channel energy. This software dose it. You can obtain input and output spectrum, noise figure, and so on. RAMAN 放大器模块结构与 EDFA 类似，其泵浦可以任意选取，增益谱可以是三角形近似形式，或者是自定义形式由文件给出，瑞利散射系数用户可以根据需要自己定义。目前泵浦还需人工设置，有关利用遗传算法优化泵浦工作正在进行当中。可提供 RAMAN 放大增益谱，信道功率沿光纤分布情况，噪声指数及信道增益。模块设计中应用了超松弛迭代技术，通过平均功率，解析积分等减少计算量。可通过设置剖分段数、迭代误差及频谱分辨率来提高模拟精度，但计算量同时也会相应增大。 RAMAN 放大器模块同样具有单独设计和系统在线应用的功能。这些都是许多商用软件所不具备的。 分布式光纤拉曼放大器具有良好的噪声特性和较宽的增益带宽 , 已经成为新一代光通信网络和长距离无中继系统中的关键技术。前向泵浦的容易受到抽运光强度和偏振不稳定性的影响。因此 , 目前 RAMAN 普遍采用后向泵浦。通常利用后向泵浦 RAMAN 放大的低噪声的特性把它作为接收机或ＥＤＦＡ的预放器已经成为一个引人注目的发展方向。另一方面 RAMAN 放大器的增益平坦度也是人们非常关心的，通过优化泵浦功率，前后数量配置，泵浦波长配置可以实现信道增益的平坦，同时要保证经济性。 RAMAN 泵浦的优化配置计算量很大，与信道数泵浦数直接相关，一般采用遗传算法进行优化 12. 光纤激光器分析包 Fiber Laser Analysis System The model of fiber laser is like that of fiber grating. Transfer matrix method is used. 13. 光电集成回路分析包 OEIC Analysis System OEIC simulation software is based on PSPICE platform, which have following features and functions: 1. Analyze directional current work point,DC,AC and transient characteristics. The device that can be processed includes semiconductor normal heterojunction laser, quantum well laser,HBT,MOSFET, linear and nonlinear elements. 2. Calculate the relation of output power and concentration of photos in the laser cavity. 3. Develop the large signal modulation modules. 4. Present a model about the parasitic capacitance of electrode and link line. 光电集成回路模型库可以运行于 PSPICE 平台，光电子器件模型包括 FP ， DFB ，量子阱及异质结半导体激光器，放大器，探测器， HBT ， MOSFET 等，可以对这些器件的等效电路，直流工作点 DC ， AC ，瞬态特性，调制特性，寄生效应进行分析建模，并可以与其它电子器件集成，进行光电混合分析。是光电集成的必备模型库。 14. 能带不连续计算包 Band Offset Analysis System Band offset module is used to analyze the conduction band and valence band position when two kinds of adjacent material has strain effects. The band offset affects energy level distribution and carrier confinement. Harrison model is applied and strain can be calculated. 能带不连续性计算模块 (Band offset) 主要用于确定相邻材料间无应变或存在应变时的带边位置。带边位置直接影响能级、增益及线宽增强因子的计算。另外通过带边位置的计算 , 我们很容易分析和设计载流子限制层。 设计中采用 Harrison 及 Model-Solid 模型 , 数据库中收集了半导体 III - V 合金化合物材料，可方便地计算相互间应变。 15. 半导体能带分析包 Energy Band Analysis System Energy band structure analysis tool is used to calculate bulk ,quantum well and super lattice structure. Gain can be obtain according to energy band structure. 2 band,4 band,6 band and 7 band model are applied. A variational approach is used to solve the problem , which considers valence band couple ,Kane matrix element ,and so on. 能带结构分析模块 (Energy band analysis) ，主要用于对体材料，量子阱，超晶格的能带结构进行分析，以计算材料增益 , 微分增益及线宽因子等参数。核心计算模块包含了 3 带， 4 带， 6 带及 8 带哈密顿矩阵形式，考虑价带耦合及应变等关键因素，采取包络函数近似及变分法求解矩阵特征值及特征向量。能带不连续性计算采用了 Model-Solid 模型和 Harrison 模型。 16. 半导体激光器一维分析包 Laser Transverse 1D Analysis System This module is used to analyze a FP quantum well laser. Layer description ,inequality grid difference, couple equations self-consistent solution and super-relaxation iteration technology are applied. You can obtain distribution of carrier ,optical field ,electric field ,electric potential ,threshold current and optical output characteristics. 横向一维分析模块 (Transverse one dimension analysis) ，主要用于分析 FP 腔量子阱激光器。对条形激光器的分析虽然不够精确，但计算速度较快。其中运用了分层描述，不等距剖分，耦合方程组自洽求解，超松弛迭代等关键技术。目前可分析载流子分布，光场分布，电势分布，阈值特性，光输出电流特性等。下面将具体介绍模型的特点及系统的功能： 1. 耦合方程组包括泊松方程，连续性方程，矢量波方程光子速率方程及 热传导方程。 2. 用热发射模型处理突变异质结处的载流子输运。 3. 利用三点有限差分格式离散微分方程式。 4. 用 Harrison 及 Model-Solid 模型计算能带不连续性；应变量子阱用 k · p 理论来处理，考虑价带混合效应 ; 用量子阱子能带来精确计算光增益 , 并考虑非线性增益抑制。 5. 非平衡载流子复合模型包括 SRH,Auger, 受激发射及自发发射复合。 6. 数据库中收集了 III - V 族合金化合物体系的材料参数。 7. 用费米统计来精确计算体材料及量子阱区载流子浓度。 8. 用不完全电离模型处理杂质电离。 9. 考虑与电场有关的迁移率模型。 10. 方程组的求解利用全耦合牛顿法及自洽求解方法 , 具体实现当中应用了超松弛迭代技术。 11. 热传导模型包括的热源有：焦耳热，非辐射复合热。 12. 可以分析半导体 FP 腔量子阱激光器的阈值特性 , 电流电压关系 (I-V) 及光功率输出特性 (L-I) 。 13. 可以给出势能、电场、电流、电子、空穴、温度分布及在各偏压下的能带图。 14. 将薛定谔方程完全解引入到自洽求解当中 , 处理量子尺寸、隧穿、量子斯塔克效应。 15. 电学方程边界条件包括欧姆接触 , 肖特基接触 , 反射边界条件及电流边界条件；波动方程边界条件包括反射边界条件及零边界条件；热传导方程边界条件包括等温，绝热及热交换边界条件。其它边界条件有待完善。 16. 激光器描述采用分层描述的方法 , 可方便地编辑材料类型、组分 , 器件几何结构。模块本身还具有不等距自动剖分及识别异质结引入热发射模型功能。 17. 半导体激光器二维分析包 Laser Transverse 2D Analysis System This module is used to analyze a FP quantum well laser. Layer description ,inequality grid difference, couple equations self-consistent solution and super-relaxation iteration technology are applied. You can obtain distribution of carrier ,optical field ,electric field ,electric potential ,threshold current and optical output characteristics. 横向二维分析模块 (Transverse two dimension analysis) ，主要用于分析 FP 腔增益和折射率波导条形半导体量子阱激光器。模块设计与一维类似，包括上节所列的全部模型及功能。不同的是微分方程是用五点差分格式离散的， 这给薛定谔方程的求解及热发射扩散模型的引入带来了困难。它可以给出二维的电子及空穴分布，光场分布，电势分布，温度分布。必须注意的是在二维结构编辑过程中 , 每一层的坐标位置非常重要，如果给错，将无法剖分，也不能进行计算。图 1 和图 2 分别给出了载流子浓度及光场的二维分布。左侧对话框为结构编辑界面，右侧视窗给出分析结果。 18. 半导体激光器纵向一二维分析包 Longitudinal one dimension analysis This module is used to analyze any kind of quantum well laser. Layer description ,inequality grid difference, couple equations self-consistent solution and super-relaxation iteration technology are applied. You can obtain distribution of carrier ,optical field ,electric field ,electric potential ,threshold current and optical output characteristics. 纵向一维分析模块 纵向一维模拟系统 (Longitudinal one dimension analysis) 是用来分析沿腔长方向激光器的一些物理量变化情况，如载流子浓度，光子浓度，有效折射率。在此基础上得到器件的一些主要特性，如振荡模式 , 阈值特性 ,L-I 曲线及 AM/FM 调制特性。计算中不考虑具体的横向结构 , 只求解纵向一维的连续性方程及耦合波方程，可以分析普通异质结及量子阱 FP ， DFB ， DBR 激光器，一些参数要用近似方法给出。优点是计算速度较快，不用编辑横向结构 , 但对于复杂结构有一定局限性。它主要采用传递矩阵方法 , 矢量法对纵模进行求解。 19. 半导体激光器三维分析包 Laser 3D Analysis System This module is used to analyze any kind of quantum well laser. Layer description ,inequality grid difference, couple equations self-consistent solution and super-relaxation iteration technology are applied. You can obtain distribution of carrier ,optical field ,electric field ,electric potential ,threshold current and optical output characteristics. 准三维分析模块 准三维模拟系统 (Quasi-three dimension simulator) 采用横向二维分析与纵向光波耦合方程求解相结合的方法设计的，可以处理各种横向二维结构，纵向上能够分析 FP, DFB ， DBR 及多段耦合腔激光器。 模块设计当中主要采用参数拟和法 , 传递矩阵及矢量法对纵模进行求解。可以分析三维载流子浓度，光场及电流分布。由此得到激光器的发射波长 , 阈值特性 ,L-I 等特性。 20. 量子阱优化包 Optimize design of multi-quantum well active zone 多量子阱有源区优化设计系统 多量子阱有源区优化设计模块 (Optimize design) 以得到低的阈值电流、阈值电流密度，高的最大工作温度及张驰振荡频率为优化条件 , 对多量子阱激光器有源区的阱宽，阱数，腔长等参数进行优化设计。 优化设计模块核心计算部分包括横向一维、二维求解模块，纵向一维分析模块及能带分析模块。优化设计是以大量计算为基础的，目前考虑可变的参量为激光器腔长、多量子阱阱数和阱宽。实际上还有许多其它可优化参数，但由于计算时间限制，不能一一优化，用户只能通过手工在所用的模块中改变这些参数，得到优化结果。 21. 金属有机物化学气相沉积热力学分析包 （ MOCVD thermodynamics analysis ） This module is designed on principle of free energy minimum, which can process multi phase system.In a IDE,it can analyze the distribution change of species due to technical parameter. The database has been built,which includes As,H,C,Ga,N,P,Cl,Ge,Si,Sb and In element. This software can process gas,liquid,solid and multi-alloy phase thermodynamic equilibrium system. 22. 多结太阳能电池设计包 Multi-junction Solar Cell Design 多结太阳能电池匹配设计对于获得最大效率尤其关键，该模块能够对多结太阳电池的能带匹配， VI 特性、效率进行仿真计算及设计，包括聚光电池，是太阳能电池研究者的理想工具。
标签: 软件包
