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Tag tools [508 articles]

Recent papers classified by the tag tools.
  • Ontological analysis of gene expression data: current tools, limitations, and open problems.
    Bioinformatics, Vol. 21, No. 18. (15 September 2005), pp. 3587-3595.
    by P Khatri, S Drăghici
    posted to microarray ontology review tools by yggdrasil on 2008-04-21 10:00:46 as ** along with 9 people marck ellakat Cortel dragonrez macavity1g Garamonfok sgoetz heliopais kristen
  • A survey of DNA motif finding algorithms
    BMC Bioinformatics, Vol. 8, No. Suppl 7. (2007)
    by Modan Das, Ho K Dai
    posted to mining motifs review tools by yevishere on 2008-01-08 00:27:21 as ** along with 6 people xili03 brant dquest nklee maximilianh csdhwang
  • TFCONES: A database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements
    BMC Genomics, Vol. 8 (29 November 2007), 441.
    by Alison P Lee, Yuchen Yang, Sydney Brenner, Byrappa Venkatesh
    posted to mining motifs tools by yevishere on 2008-01-08 00:26:52 as ** along with 3 people jyuh nklee maximilianh
  • Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions
    BMC Bioinformatics, Vol. 8, No. 1. (2007)
    by Victor Levitsky, Elena Ignatieva, Elena Ananko, Igor Turnaev, Tatyana Merkulova, Nikolay Kolchanov, T Hodgman
    posted to mining motifs tools by yevishere on 2008-01-08 00:22:02 as **** along with 4 people xili03 nklee maximilianh csdhwang
  • Toucan: deciphering the cis-regulatory logic of coregulated genes.
    Nucleic Acids Res, Vol. 31, No. 6. (15 March 2003), pp. 1753-1764.
    by S Aerts, G Thijs, B Coessens, M Staes, Y Moreau, B De Moor
    posted to mining motifs tools by yevishere on 2008-01-08 00:20:26 as ** along with 5 people and 1 group troels_marstrand kaspermunch nur77 nklee xili03 Bioinformatics
  • A survey of motif discovery methods in an integrated framework
    Biology Direct, Vol. 1, No. 1. (06 April 2006), 11.
    by Geir K Sandve, Finn Drabløs
    posted to mining motifs tools by yevishere on 2008-01-04 00:23:12 as ** along with 4 people and 1 group aprasad dpollard samal csdhwang EisenLab
  • Discovering Motifs in Ranked Lists of DNA Sequences
    PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e39.
    by Eran Eden, Doron Lipson, Sivan Yogev, Zohar Yakhini
    posted to motifs tools by yevishere on 2008-01-04 00:22:30 as ** along with 3 people and 1 group chad_davis dpollard dquest EisenLab
  • A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites.
    Nucleic Acids Res, Vol. 34, No. 20. (2006), pp. 5730-5739.
    by BT Naughton, E Fratkin, S Batzoglou, DL Brutlag
    posted to motifs tools by yevishere on 2008-01-04 00:20:45 as **** along with 3 people and 1 group xili03 indigoviolet nklee EisenLab
  • GOstat: find statistically overrepresented Gene Ontologies within a group of genes.
    Bioinformatics, Vol. 20, No. 9. (12 June 2004), pp. 1464-1465.
    by T Beissbarth, TP Speed
    posted to tools by yevishere on 2008-01-04 00:19:57 as ** along with 6 people and 1 group ellakat Yanno miguel RMGraze indigoviolet jdiggans EisenLab
  • Sequence logos: a new way to display consensus sequences.
    Nucleic Acids Res, Vol. 18, No. 20. (25 October 1990), pp. 6097-6100.
    by TD Schneider, RM Stephens
    posted to tools by yevishere on 2008-01-04 00:19:33 as ** along with 3 people and 1 group austin analogAI indigoviolet EisenLab
  • WebLogo: A Sequence Logo Generator
    Genome Res., Vol. 14, No. 6. (1 June 2004), pp. 1188-1190.
    by Gavin E Crooks, Gary Hon, John-Marc Chandonia, Steven E Brenner
    posted to tools by yevishere on 2008-01-04 00:16:26 as ** along with 4 people and 2 groups analogAI indigoviolet xiaobeizhao sobolevnrm EisenLab baker-group
  • notes LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA.
    Genome Res, Vol. 13, No. 4. (April 2003), pp. 721-731.
    by M Brudno, CB Do, GM Cooper, MF Kim, E Davydov, ED Green, A Sidow, S Batzoglou,
    posted to genome_alignment tools by xwbcn on 2006-01-04 08:58:23 as ** along with 12 people and 1 group Neeperando operon balajis dpollard dquest adepace hdopazo lusk Garamonfok adijr natstreet nklee EisenLab
  • Past, present, and future of user interface software tools
    ACM Trans. Comput.-Hum. Interact., Vol. 7, No. 1. (March 2000), pp. 3-28.
    by Brad Myers, Scott E Hudson, Randy Pausch
    posted to tools ui by wigelius on 2006-12-10 20:02:54 as *** along with 7 people and 4 groups kgajos luiinge noahwf ahmedshafi ianli hcii-cs-mini flgeyer CMU-HCII 2ndFloor HCI-IHTE-TUT hcii-areas
  • notes Wikis: Tools for Information Work And Collaboration: Tools for Information Work And Collaboration (Information Professional S.)
    (30 May 2005)
    by Jane Klobas
    posted to collaboration sebastien_paquet tools wikis by wcrosbie on 2006-07-31 05:53:25 as ** along with 4 people and 2 groups domt rickl soph41 AnneB Wikipedia CoP_CMS
  • imergo: Supporting Accessibility and Web Standards to Meet the Needs of the Industry via Process-Oriented Software Tools
    : Computers Helping People with Special Needs (2004), pp. 310-316.
    by Yehya Mohamad, Dirk Stegemann, Johannes Koch, Carlos A Velasco
    posted to tools quality_assurance accessibility by velasco on 2007-01-27 14:12:35 as read
  • Kommunikation im Chat: Grundlagen, Instrumente, Bewertung
    (2005)
    by Annegret Teplan
    posted to tools chat 2005 by Torsten_Holmer on 2008-07-01 14:01:33 as **
  • TACCLE: a methodology for object-oriented software testing at the class and cluster levels
    ACM Trans. Softw. Eng. Methodol., Vol. 10, No. 1. (January 2001), pp. 56-109.
    by Huo Y Chen, TH Tse, TY Chen
    posted to blackbox class-level-testing cluster-level-testing equivalence-testing object-oriented testing tools unit-testing whitebox by tinkha on 2005-03-17 08:57:59 as *** along with 1 group Context-driven-testers
  • Passive visual fingerprinting of network attack tools
    (2004), pp. 45-54.
    by Gregory Conti, Kulsoom Abdullah
    posted to attack fingerprinting network tools by thonnardo on 2006-06-25 21:04:06 as **** along with 1 person knowlengr
  • UniPrime: a workflow-based platform for improved universal primer design
    Nucl. Acids Res., Vol. 36, No. 10. (1 June 2008), e56.
    by Michael Bekaert, Emma C Teeling
    posted to tools primers genbank bioinformatics by tharris on 2008-06-11 12:26:00 as ** along with 3 people and 1 group niallhaslam jyuh stajich Berkeley Mycology
  • OBO Explorer: an editor for open biomedical ontologies in OWL
    Bioinformatics, Vol. 24, No. 3. (1 February 2008), pp. 443-444.
    by Stuart Aitken, Yin Chen, Jonathan Bard
    posted to tools owl ontology obo methods by tharris on 2008-06-20 17:06:27 as ** along with 3 people jyuh dullhunk lenov
  • Static source code checking for user-defined properties
    Proc. IDPT 2002 (2002)
    by GJ Holzmann
    posted to idpt02 model_checking tools uno by srccheck on 2008-02-08 12:13:54 as *****
  • Improving Security Using Extensible Lightweight Static Analysis
    IEEE Software, Vol. 19, No. 1. (\slash 2002), pp. 42-51.
    by David Evans, David Larochelle
    posted to splint static_analysis tools by srccheck on 2008-02-08 11:55:04 as read
  • A First Step towards Automated Detection of Buffer Overrun Vulnerabilities
    (February 2000), pp. 3-17.
    by David Wagner, Jeffrey S Foster, Eric A Brewer, Alexander Aiken
    posted to boon buffer_overflow constraint_analysis ndss00 tools by srccheck on 2008-02-08 11:46:21 as read along with 2 people martink roylee
  • A Comparison of Publicly Available Tools for Static Intrusion Prevention
    (November 2002), pp. 68-84.
    by John Wilander, Mariam Kamkar
    posted to benchmark boon flawfinder its4 rats splint survey tools by srccheck on 2008-02-08 11:33:16 as **** along with 3 people mercutio radical V
  • ARCHER: using symbolic, path-sensitive analysis to detect memory access errors
    (2003), pp. 327-336.
    by Yichen Xie, Andy Chou, Dawson R Engler
    posted to archer path_sensitive tools by srccheck on 2008-02-08 11:24:47 as ****
  • Testing static analysis tools using exploitable buffer overflows from open source code
    (2004), pp. 97-106.
    by Misha Zitser, Richard Lippmann, Tim Leek
    posted to archer benchmark boon fse04 polyspace splint survey tools uno by srccheck on 2008-02-08 10:53:26 as read
  • Taming False Alarms from a Domain-Unaware C Analyzer by a Bayesian Statistical Post Analysis
    Static Analysis (2005), pp. 203-217.
    by Yungbum Jung, Jaehwang Kim, Jaeho Shin, Kwangkeun Yi
    posted to airac machine_learning sas05 static_analysis tools warning_ranking by srccheck on 2008-02-08 10:33:57 as read
  • Lazy abstraction
    SIGPLAN Not., Vol. 37, No. 1. (January 2002), pp. 58-70.
    by Thomas A Henzinger, Ranjit Jhala, Rupak Majumdar, Grégoire Sutre
    posted to blast model_checking tools by srccheck on 2008-04-07 12:12:50 as read along with 1 person bfraser
  • Extended static checking for Java
    (2002)
    by C Flanagan, K Leino, M Lillibridge, C Nelson, J Saxe, R Stata
    posted to esc java pldi02 static_analysis tools by srccheck on 2008-04-02 11:14:21 as read along with 2 people and 2 groups amorkan sjgaller Context-driven-testers Desgin-by-Contract
  • Code Injection in C and C++: A Survey of Vulnerabilities and Countermeasures
    No. CW386. (July 2004)
    by Yves Younan, Wouter Joosen, Frank Piessens
    posted to vulnerabilities tools survey defects by srccheck on 2008-05-08 12:02:14 as ***
  • Checking System Rules Using System-Specific, Programmer-Written Compiler Extensions
    (October 2000)
    by D Engler, B Chelf, A Chou, S Hallem
    posted to defects mc osdi00 tools by srccheck on 2008-02-06 10:34:50 as read
  • Scalable error detection using boolean satisfiability
    SIGPLAN Not., Vol. 40, No. 1. (January 2005), pp. 351-363.
    by Yichen Xie, Alex Aiken
    posted to popl05 saturn tools by srccheck on 2008-02-06 14:44:06 as **** along with 1 person plaugg
  • A static analyzer for finding dynamic programming errors
    Softw. Pract. Exper., Vol. 30, No. 7. (2000), pp. 775-802.
    by William R Bush, Jonathan D Pincus, David J Sielaff
    posted to defect_search prefix to_close tools by srccheck on 2008-02-06 09:45:35 as read along with 1 person ronnix
  • Bugs as Inconsistent Behavior: A General Approach to Inferring Errors in Systems Code
    (2001), pp. 57-72.
    by Dawson R Engler, David Y Chen, Andy Chou
    posted to defects defect_search inconsistent_code mc sosp01 to_close tools by srccheck on 2008-02-06 09:27:57 as read along with 3 people gameweld ronnix bdanilov
  • Finding bugs is easy
    SIGPLAN Not., Vol. 39, No. 12. (December 2004), pp. 92-106.
    by David Hovemeyer, William Pugh
    posted to tools templates findbugs by srccheck on 2008-04-17 07:23:58 as **** along with 2 people and 2 groups ronison linekin Oracle_10g_Group GMF-UFCG
  • Detecting format string vulnerabilities with type qualifiers
    (2001), pp. 16-16.
    by Umesh Shankar, Kunal Talwar, Jeffrey S Foster, David Wagner
    posted to annotations extended_types format_string tools by srccheck on 2008-04-02 14:18:10 as **
  • Large-scale analysis of format string vulnerabilities in Debian Linux
    (2007), pp. 75-84.
    by Karl Chen, David Wagner
    posted to oink pldi07 search_report tools by srccheck on 2008-02-06 14:28:52 as *** along with 1 person torens
  • ITS4: a static vulnerability scanner for C and C++ code
    Computer Security Applications, 2000. ACSAC '00. 16th Annual Conference (2000), pp. 257-267.
    by J Viega, JT Bloch, Y Kohno, G Mcgraw
    posted to acsac00 its4 tools usage_warning_tools by srccheck on 2008-02-06 13:48:11 as read
  • A static analyzer for large safety-critical software
    (2003), pp. 196-207.
    by Bruno Blanchet, Patrick Cousot, Radhia Cousot, Jérome Feret, Laurent Mauborgne, Antoine Miné, David Monniaux, Xavier Rival
    posted to abstract_interpretation astree pldi03 tools by srccheck on 2008-02-08 13:29:44 as **
  • CSSV: towards a realistic tool for statically detecting all buffer overflows in C
    SIGPLAN Not., Vol. 38, No. 5. (May 2003), pp. 155-167.
    by Nurit Dor, Michael Rodeh, Mooly Sagiv
    posted to buffer_overflow cssv tools by srccheck on 2008-02-08 13:25:38 as read
  • MECA: an Extensible, Expressive System and Language for Statically Checking Security Properties
    (2003)
    by Junfeng Yang, Ted Kremenek, Yichen Xie, Dawson Engler
    posted to meca static_analysis tools by srccheck on 2008-02-12 16:25:10 as ****
  • LCLint: a tool for using specifications to check code
    SIGSOFT Softw. Eng. Notes, Vol. 19, No. 5. (December 1994), pp. 87-96.
    by David Evans, John Guttag, James Horning, Yang M Tan
    posted to lclint static_analysis tools by srccheck on 2008-02-11 11:01:46 as *****
  • Thorough static analysis of device drivers
    SIGOPS Oper. Syst. Rev., Vol. 40, No. 4. (October 2006), pp. 73-85.
    by Thomas Ball, Ella Bounimova, Byron Cook, Vladimir Levin, Jakob Lichtenberg, Con Mcgarvey, Bohus Ondrusek, Sriram K Rajamani, Abdullah Ustuner
    posted to model_checking slam tools by srccheck on 2008-04-07 12:23:24 as **
  • On the automatic modularization of software systems using the Bunch tool
    Software Engineering, IEEE Transactions on, Vol. 32, No. 3. (2006), pp. 193-208.
    by BS Mitchell, S Mancoridis
    posted to tools by smogit on 2007-06-08 11:18:37 as **
  • Toward the Next Generation of Data Modeling Tools
    Software Engineering, IEEE Transactions on, Vol. SE-11, No. 9. (1985), pp. 966-970.
    by CR Carlson, AK Arora
    posted to tools by smogit on 2007-06-08 11:15:24 as **
  • The SEXTANT Software Exploration Tool
    Software Engineering, IEEE Transactions on, Vol. 32, No. 9. (2006), pp. 753-768.
    by T Schafer, M Eichberg, M Haupt, M Mezini
    posted to tools by smogit on 2007-06-08 11:10:59 as ** along with 3 people hawkestein emerson duckysherwood
  • A compiler for analyzing cryptographic protocols using noninterference
    ACM Trans. Softw. Eng. Methodol., Vol. 9, No. 4. (October 2000), pp. 488-528.
    by Antonio Durante, Riccardo Focardi, Roberto Gorrieri
    posted to tools by smogit on 2007-06-08 11:07:09 as **
  • HOTTest: A model-based test design technique for enhanced testing of domain-specific applications
    ACM Trans. Softw. Eng. Methodol., Vol. 15, No. 3. (July 2006), pp. 242-278.
    by Avik Sinha, Carol Smidts
    posted to tools by smogit on 2007-06-08 09:39:53 as ** along with 1 person and 1 group oscar onekin
  • Flexible consistency checking
    ACM Trans. Softw. Eng. Methodol., Vol. 12, No. 1. (January 2003), pp. 28-63.
    by Christian Nentwich, Wolfgang Emmerich, Anthony Finkelstein, Ernst Ellmer
    posted to tools by smogit on 2007-06-08 09:38:26 as ** along with 1 person asilva
  • The Control Structure Diagram: An Overview and Initial Evaluation
    Empirical Software Engineering, Vol. 3, No. 2. (1 June 1998), pp. 131-158.
    by James H Cross, Dean T Hendrix, Saeed Maghsoodloo
    posted to tools by smogit on 2007-06-08 09:29:28 as **
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