-
1
-
-
45949109669
-
MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences
-
Kumar S, Nei M, Dudley J, Tamura K (2008) MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 9: 299-306.
-
(2008)
Brief Bioinform
, vol.9
, pp. 299-306
-
-
Kumar, S.1
Nei, M.2
Dudley, J.3
Tamura, K.4
-
2
-
-
33751381461
-
Time-Tree: A public knowledge-base of divergence times among organisms
-
Hedges SB, Dudley J, Kumar S (2006) Time-Tree: a public knowledge-base of divergence times among organisms. Bioinformatics (Oxford, England) 22: 2971-2972.
-
(2006)
Bioinformatics (Oxford, England)
, vol.22
, pp. 2971-2972
-
-
Hedges, S.B.1
Dudley, J.2
Kumar, S.3
-
3
-
-
34547763724
-
Bioinformatics software for biologists in the genomics era
-
Kumar S, Dudley J (2007) Bioinformatics software for biologists in the genomics era. Bioinformatics (Oxford, England) 23: 1713-1717.
-
(2007)
Bioinformatics (Oxford, England)
, vol.23
, pp. 1713-1717
-
-
Kumar, S.1
Dudley, J.2
-
4
-
-
35748982114
-
AILUN: Reannotating gene expression data automatically
-
Chen R, Li L, Butte AJ (2007) AILUN: reannotating gene expression data automatically. Nature Methods 4: 879-879.
-
(2007)
Nature Methods
, vol.4
, pp. 879-879
-
-
Chen, R.1
Li, L.2
Butte, A.J.3
-
5
-
-
62349088493
-
-
Chen R, Ma l l elwar R, Thosar A, Venkatasubrahmanyam S, Butte AJ (2008) GeneChaser: identifying all biological and clinical conditions in which genes of interest are differentially expressed. BMC Bioinformatics 9: 548.
-
Chen R, Ma l l elwar R, Thosar A, Venkatasubrahmanyam S, Butte AJ (2008) GeneChaser: identifying all biological and clinical conditions in which genes of interest are differentially expressed. BMC Bioinformatics 9: 548.
-
-
-
-
6
-
-
0037433696
-
PGAGENE: Integrating quantitative gene-specific results from the NHLBI programs for genomic applications
-
Lee K, Kohane IS, Butte AJ (2003) PGAGENE: integrating quantitative gene-specific results from the NHLBI programs for genomic applications. Bioinformatics (Oxford, England) 19: 778-779.
-
(2003)
Bioinformatics (Oxford, England)
, vol.19
, pp. 778-779
-
-
Lee, K.1
Kohane, I.S.2
Butte, A.J.3
-
7
-
-
74549137157
-
-
The R Project for Statistical Computing [http:// www.R-project.org/].
-
-
-
-
9
-
-
74549188847
-
-
Perl.org [http://www.perl.org/].
-
Perl.org
-
-
-
12
-
-
0003939246
-
-
Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. xii, 692 p
-
Mount DW (2004) Bioinformatics: sequence and genome analysis. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. xii, 692 p.
-
(2004)
Bioinformatics: Sequence and genome analysis
-
-
Mount, D.W.1
-
13
-
-
74549120073
-
-
Tisdall J (2001) Beginning perl for bioinformatics O'Reilly Media, Inc.
-
Tisdall J (2001) Beginning perl for bioinformatics O'Reilly Media, Inc.
-
-
-
-
15
-
-
74549185579
-
-
Tisdall JD (2003) Mastering perl for bioinformatics O'Reilly Media, Inc.
-
Tisdall JD (2003) Mastering perl for bioinformatics O'Reilly Media, Inc.
-
-
-
-
17
-
-
74549219673
-
-
Model M (2009) Bioinformatics programming using python O'Reilly Media, Inc.
-
Model M (2009) Bioinformatics programming using python O'Reilly Media, Inc.
-
-
-
-
18
-
-
74549215485
-
-
RPy home page [http://rpy.sourceforge.net/].
-
RPy home page [http://rpy.sourceforge.net/].
-
-
-
-
19
-
-
74549124116
-
-
JRuby [http://jruby.codehaus.org/].
-
JRuby
-
-
-
24
-
-
1842845736
-
The Bio* toolkits-a brief overview
-
Mangalam H (2002) The Bio* toolkits-a brief overview. Brief Bioinform 3: 296-302.
-
(2002)
Brief Bioinform
, vol.3
, pp. 296-302
-
-
Mangalam, H.1
-
25
-
-
18644368714
-
The Bioperl toolkit: Perl modules for the life sciences
-
Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, et al. (2002) The Bioperl toolkit: perl modules for the life sciences. Genome Res 12: 1611-1618.
-
(2002)
Genome Res
, vol.12
, pp. 1611-1618
-
-
Stajich, J.E.1
Block, D.2
Boulez, K.3
Brenner, S.E.4
Chervitz, S.A.5
-
26
-
-
40549105825
-
An introduction to BioPerl
-
Stajich JE (2007) An introduction to BioPerl. Methods Mol Biol 406: 535-548.
-
(2007)
Methods Mol Biol
, vol.406
, pp. 535-548
-
-
Stajich, J.E.1
-
27
-
-
65649092976
-
Biopython: Freely available Python tools for computational molecular biology and bioinformatics
-
Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, et al. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25: 1422-1423.
-
(2009)
Bioinformatics
, vol.25
, pp. 1422-1423
-
-
Cock, P.J.1
Antao, T.2
Chang, J.T.3
Chapman, B.A.4
Cox, C.J.5
-
28
-
-
74549178885
-
-
BioRuby [http://www.bioruby.org].
-
BioRuby
-
-
-
29
-
-
68949101334
-
An introduction to scripting in Ruby for biologists
-
Aerts J, Law A (2009) An introduction to scripting in Ruby for biologists. BMC Bioinformatics 10: 221.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 221
-
-
Aerts, J.1
Law, A.2
-
30
-
-
51749088608
-
BioJava: An open-source framework for bioinformatics
-
Holland RCG, Down TA, Pocock M, Prlić A, Huen D, et al. (2008) BioJava: an open-source framework for bioinformatics. Bioinformatics (Oxford, England) 24: 2096-2097.
-
(2008)
Bioinformatics (Oxford, England)
, vol.24
, pp. 2096-2097
-
-
Holland, R.C.G.1
Down, T.A.2
Pocock, M.3
Prlić, A.4
Huen, D.5
-
31
-
-
28744458859
-
Bioconductor: Open software development for computational biology and bioinformatics
-
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80.
-
(2004)
Genome Biol
, vol.5
-
-
Gentleman, R.C.1
Carey, V.J.2
Bates, D.M.3
Bolstad, B.4
Dettling, M.5
-
32
-
-
74549216267
-
-
SciPy [http://www.scipy.org/].
-
SciPy
-
-
-
33
-
-
74549146015
-
-
Home
-
Numpy Home Page [http://numpy.scipy.org/].
-
Numpy
-
-
-
34
-
-
56549121497
-
-
Ruby on Rails [http://rubyonrails.org/].
-
Ruby on Rails
-
-
-
36
-
-
74549171928
-
-
Ubuntu [http://www.ubuntu.com].
-
Ubuntu
-
-
-
37
-
-
74549215484
-
-
BioBrew Linux [http://biobrew.bioinformatics. org].
-
BioBrew Linux
-
-
-
38
-
-
74549150920
-
-
Cygwin [http://www.cygwin.com/].
-
Cygwin
-
-
-
39
-
-
74549175569
-
-
Doxygen [http://www.stack.nl/~dimitri/doxygen/].
-
Doxygen
-
-
-
40
-
-
84858500994
-
-
Javadoc Tool [http://java.sun.com/j2se/javadoc/].
-
Javadoc Tool
-
-
-
41
-
-
74549134392
-
-
Pydoc [http://docs.python.org/library/pydoc].
-
Pydoc
-
-
-
42
-
-
74549181786
-
-
Naming conventions (programming) [http:// en.wikipedia.org/w/index.php? title =Naming- conventions-(programming)&oldid=302546480].
-
Naming conventions (programming) [http:// en.wikipedia.org/w/index.php? title =Naming- conventions-(programming)&oldid=302546480].
-
-
-
-
43
-
-
74549148759
-
-
GNU make [http://www.gnu.org/software/ make/manual/html-node/index.html].
-
GNU make
-
-
-
44
-
-
68049110535
-
-
Apache Ant [http://ant.apache.org/].
-
Apache Ant
-
-
-
46
-
-
74549218251
-
-
Rake - Ruby Make [http://rake.rubyforge.org/].
-
Ruby Make
-
-
-
48
-
-
74549208353
-
-
Subversion [http://subversion.tigris.org/].
-
Subversion [http://subversion.tigris.org/].
-
-
-
-
49
-
-
74549223437
-
-
Git - Fast Version Control System [http:// git-scm.com/].
-
Git - Fast Version Control System [http:// git-scm.com/].
-
-
-
-
50
-
-
81455154203
-
-
TortoiseSVN [http://tortoisesvn.net/].
-
TortoiseSVN
-
-
-
51
-
-
74549163145
-
-
SCPlugin [http://scplugin.tigris.org/].
-
SCPlugin
-
-
-
52
-
-
74549183310
-
-
SourceForge
-
SourceForge.
-
-
-
-
53
-
-
74549116257
-
-
GitHub
-
GitHub.
-
-
-
-
54
-
-
74549146605
-
-
Mozy.com [http://mozy.com/].
-
Mozy.com
-
-
-
55
-
-
74549123083
-
-
IDrive [http://www.idrive.com].
-
IDrive
-
-
-
56
-
-
74549119290
-
-
TimeVault Project
-
TimeVault Project.
-
-
-
-
57
-
-
84870669691
-
-
Sun Grid Engine [http://gridengine.sunsource. net/].
-
Sun Grid Engine
-
-
-
58
-
-
74549118723
-
-
PBS GridWorks: OpenPBS [http://www. pbsgridworks.com/].
-
OpenPBS
-
-
-
59
-
-
84871120375
-
-
Message Passing Interface [http://en.wikipedia.org/w/ index.php?title=Message-Passing-Interface&oldid= 304813355].
-
Message Passing Interface
-
-
-
60
-
-
37549003336
-
Mapreduce: Simplified data processing on large clusters
-
Dean J, Ghemawat S (2008) Mapreduce: Simplified data processing on large clusters. Communications of the Acm 51: 107-113.
-
(2008)
Communications of the Acm
, vol.51
, pp. 107-113
-
-
Dean, J.1
Ghemawat, S.2
-
61
-
-
84870452716
-
-
Apache Hadoop [http://hadoop.apache.org/].
-
Apache Hadoop
-
-
-
62
-
-
74549225499
-
-
Disco [http://discoproject.org/].
-
Disco
-
-
-
63
-
-
74549210455
-
-
Skynet [http://skynet.rubyforge.org/].
-
Skynet
-
-
-
65
-
-
65649120715
-
CloudBurst: Highly sensitive read mapping with MapReduce
-
Schatz MC (2009) CloudBurst: highly sensitive read mapping with MapReduce. Bioinformatics 25: 1363-1369.
-
(2009)
Bioinformatics
, vol.25
, pp. 1363-1369
-
-
Schatz, M.C.1
-
66
-
-
74549205071
-
-
Amazon Elastic Compute Cloud (EC2).
-
Amazon Elastic Compute Cloud (EC2).
-
-
-
-
67
-
-
74549150786
-
-
Cancer Biomedical Informatics Grid
-
Cancer Biomedical Informatics Grid.
-
-
-
-
68
-
-
74549173361
-
-
MySQL [http://www.mysql.com/].
-
-
-
-
69
-
-
74549140110
-
-
Active Record [http://ar.rubyonrails.org/].
-
Active Record
-
-
-
70
-
-
74549212349
-
-
SQLObject [http://www.sqlobject.org/].
-
SQLObject
-
-
-
71
-
-
74549142196
-
-
DBIx-Class [http://search.cpan.org/dist/DBIx-Class/].
-
DBIx-Class [http://search.cpan.org/dist/DBIx-Class/].
-
-
-
-
72
-
-
74549140109
-
-
HBase [http://hadoop.apache.org/hbase/].
-
HBase
-
-
-
73
-
-
74549134989
-
-
Hypertable [http://www.hypertable.org/].
-
Hypertable
-
-
-
74
-
-
84887349351
-
-
Cassandra Project [http://incubator.apache. org/cassandra/].
-
Cassandra Project
-
-
-
76
-
-
74549189850
-
-
MongoDB [http://www.mongodb.org].
-
MongoDB
-
-
-
78
-
-
74549167060
-
-
YOKOFAKUN
-
YOKOFAKUN: CouchDB for Bioinformatics: Storing SNPs [http://plindenbaum. blogspot.com/ 2009/04/couchdb-for-bioinformatics-storing-snps. html].
-
CouchDB for Bioinformatics: Storing SNPs
-
-
-
79
-
-
74549221250
-
Speedup bioinformatics applications on multicore-based processor using vectorizing and multithreading strategies
-
Chaichoompu K, Kittitornkun S, Tongsima S (2007) Speedup bioinformatics applications on multicore-based processor using vectorizing and multithreading strategies. Bioinformation 2: 182-184.
-
(2007)
Bioinformation
, vol.2
, pp. 182-184
-
-
Chaichoompu, K.1
Kittitornkun, S.2
Tongsima, S.3
-
80
-
-
33846697176
-
Striped Smith-Waterman speeds database searches six times over other SIMD implementations
-
Farrar M (2007) Striped Smith-Waterman speeds database searches six times over other SIMD implementations. Bioinformatics (Oxford, England) 23: 156-161.
-
(2007)
Bioinformatics (Oxford, England)
, vol.23
, pp. 156-161
-
-
Farrar, M.1
-
82
-
-
0033743209
-
Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors
-
Rognes T, Seeberg E (2000) Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors. Bioinformatics 16: 699-706.
-
(2000)
Bioinformatics
, vol.16
, pp. 699-706
-
-
Rognes, T.1
Seeberg, E.2
-
83
-
-
0035312251
-
ParAlign: A parallel sequence alignment algorithm for rapid and sensitive database searches
-
Rognes T (2001) ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches. Nucleic Acids Res 29: 1647-1652.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 1647-1652
-
-
Rognes, T.1
-
84
-
-
74549190423
-
-
CUDA Zone [http://www.nvidia.com/object/cuda-home.html#].
-
CUDA Zone [http://www.nvidia.com/object/cuda-home.html#].
-
-
-
-
85
-
-
74549208352
-
-
OpenCL [http://www.khronos.org/opencl/].
-
OpenCL
-
-
-
87
-
-
74549205661
-
CU-DASW++: Optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units
-
Liu Y, Maskell DL, Schmidt B (2009) CU-DASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units. BMC Research Notes 2: 73-73.
-
(2009)
BMC Research Notes
, vol.2
, pp. 73-73
-
-
Liu, Y.1
Maskell, D.L.2
Schmidt, B.3
-
88
-
-
64649105762
-
Accelerating molecular dynamic simulation on graphics processing units
-
Friedrichs MS, Peter E, Vishal V, Mike H, Scott L, et al. (2009) Accelerating molecular dynamic simulation on graphics processing units. J Comp Chem 30: 864-872.
-
(2009)
J Comp Chem
, vol.30
, pp. 864-872
-
-
Friedrichs, M.S.1
Peter, E.2
Vishal, V.3
Mike, H.4
Scott, L.5
-
89
-
-
74549211096
-
-
gputools package for R [http://cran.r-project. org/web/packages/gputools/ index.html].
-
gputools package for R [http://cran.r-project. org/web/packages/gputools/ index.html].
-
-
-
-
90
-
-
74549181934
-
-
pystream [http://code.google.com/p/pystream/].
-
pystream [http://code.google.com/p/pystream/].
-
-
-
-
91
-
-
34347225963
-
160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA)
-
Li ITS, Shum W, Truong K (2007) 160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA). BMC Bioinformatics 8: 185-185.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 185-185
-
-
Li, I.T.S.1
Shum, W.2
Truong, K.3
-
93
-
-
24044471657
-
Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW
-
Oliver T, Schmidt B, Nathan D, Clemens R, Maskell D (2005) Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW. Bioinformatics (Oxford, England) 21: 3431-3432.
-
(2005)
Bioinformatics (Oxford, England)
, vol.21
, pp. 3431-3432
-
-
Oliver, T.1
Schmidt, B.2
Nathan, D.3
Clemens, R.4
Maskell, D.5
-
94
-
-
43049179828
-
Explicit design of FPGA-based coprocessors for short-range force computations in molecular dynamics simulations
-
Gu Y, Vancourt T, Herbordt MC (2008) Explicit design of FPGA-based coprocessors for short-range force computations in molecular dynamics simulations. Parallel Comput 34: 261-277.
-
(2008)
Parallel Comput
, vol.34
, pp. 261-277
-
-
Gu, Y.1
Vancourt, T.2
Herbordt, M.C.3
-
95
-
-
34147119654
-
Hardware acceleration of processing of mass spectrometric data for proteomics
-
Bogdan I, Coca D, Rivers J, Beynon RJ (2007) Hardware acceleration of processing of mass spectrometric data for proteomics. Bioinformatics (Oxford, England) 23: 724-731.
-
(2007)
Bioinformatics (Oxford, England)
, vol.23
, pp. 724-731
-
-
Bogdan, I.1
Coca, D.2
Rivers, J.3
Beynon, R.J.4
-
96
-
-
74549201432
-
-
JSON [http://www.json.org/].
-
JSON [http://www.json.org/].
-
-
-
-
100
-
-
0345863927
-
The Unified Medical Language System (UMLS): Integrating biomedical terminology
-
Bodenreider O (2004) The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res 32: D267-D270.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Bodenreider, O.1
-
101
-
-
35948989284
-
The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration
-
Smith B, Ashburner M, Rosse C, Bard J, Bug W, et al. (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 25: 1251-1255.
-
(2007)
Nat Biotechnol
, vol.25
, pp. 1251-1255
-
-
Smith, B.1
Ashburner, M.2
Rosse, C.3
Bard, J.4
Bug, W.5
-
102
-
-
67849128700
-
BioPortal: Ontologies and integrated data resources at the click of a mouse
-
Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, et al. (2009) BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res 37: W170-W173.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Noy, N.F.1
Shah, N.H.2
Whetzel, P.L.3
Dai, B.4
Dorf, M.5
|