. 2012 Jun 14;40(Web Server issue):W3–W12. doi: 10.1093/nar/gks632

Table 1.

Historical summary of the number of resources, databases and web server tools listed in each subcategory of the Bioinformatics Links Directory between 2005 and 2012

Name	2005 Total	2006 Total	2007 Total	2008 Total	2009 Total	2010 Total	2011				2012^a
Name	2005 Total	2006 Total	2007 Total	2008 Total	2009 Total	2010 Total	Resources	Databases	Tools	Total	Resources	Databases	Tools	Total
Computer related
Bio-* programming tools	20	20	20	20	20	18	6		12	18	6		12	18
C/C++	3	3	3	3	3	2	1		1	2	1		1	2
Databases	2	2	2	2	3	5		1	5	6		1	5	6
Java	4	4	4	4	4	4	3		1	4	3		1	4
Linux/Unix	12	12	11	11	11	10	5	1	4	10	5	1	4	10
PERL	5	5	5	5	5	5	4		1	5	4		1	5
PHP	3	3	1	1	1	1			1	1			1	1
Statistics	9	9	9	9	9	9	2		7	9	2		7	9
Web development	6	6	2	2	2	2	2			2	2			2
Web services	5	6	7	7	10	17	3		16	19	3		15	18
Workflows						3	1		5	6	1		7	8
DNA
Annotations	29	38	56	57	62	71	1	7	65	73	1	6	59	66
Databases								56		56		54	2	56
DNA and genomic analysis	17	19	20	23	24	25	5	1	22	28	5	1	26	32
Gene prediction	17	32	33	34	37	37	1	1	35	37	1	1	29	31
Mapping and assembly	12	14	15	15	17	20	3	2	16	21	3	2	11	16
Phylogeny reconstruction	24	37	43	46	49	53	4	4	45	53	4	4	41	49
Sequence polymorphisms	22	32	39	41	42	44	1	8	39	48	1	7	39	47
Sequence retrieval and submission	23	26	30	32	32	30	1	6	23	30	1	7	20	28
Structure and sequence feature detection	71	118	142	145	150	161	3	10	150	163	3	9	137	149
Tools for the bench	44	55	63	65	71	76	2	7	67	76	2	4	60	66
Education
Bioinformatics-related news sources	9	9	9	9	9	9	9			9	7			7
Community	19	19	24	23	23	18	17		2	19	17	1	1	19
Courses, programs and workshops	5	5	5	5	5	4	3			3	1			1
Directories and portals	12	15	15	15	15	18	12		6	18	12	1	5	18
General	15	15	14	14	14	14	13	1		14	12	1		13
Tutorials and directed learning resources	9	9	9	9	9	10	10			10	9			9
Expression
cDNA, EST, SAGE	24	29	36	44	48	49	1	10	38	49	1	8	29	38
Databases								21		21		20	3	20
Gene regulation	59	96	119	120	128	138	3	16	127	146	3	16	119	138
Gene set analysis					11	24		1	29	30		1	32	33
Networks				8	12	16		2	15	17		1	21	22
Protein expression	7	8	9	17	22	23	1	3	18	22	1	2	18	21
Splicing	9	16	19	19	21	22		3	17	20		3	16	19
Transcript expression and microarrays	54	75	89	101	108	121	5	10	107	122	5	9	96	110
Human genome
Annotations	22	31	37	38	39	46	2	5	39	46	2	4	35	41
Databases								31	1	32		30	2	32
Ethics	7	7	8	8	8	6	5	1		6	4	1		5
Genomics	4	4	3	3	10	19	3	2	15	20	3	2	16	21
Health and disease	11	14	19	23	27	29	1	7	23	31	1	7	24	32
Other resources	22	25	29	29	29	31	9	4	17	30	9	4	16	29
Sequence polymorphisms	17	25	33	36	38	46	2	4	43	49	2	4	44	50
Literature
Databases								7		7		7		7
Goldmines	5	6	6	6	6	5	1	4		5	1	4		5
Open access resources	2	2	2	2	3	4	1	3		4	1	3		4
Search tools	6	10	12	12	13	14		6	8	14		6	6	12
Text mining	7	11	15	22	30	31		4	30	34		4	35	39
Model organisms
Databases								95		95		94	1	94
Fish	11	11	11	11	11	11		5	6	11		4	5	9
Fly	12	16	17	17	17	21	2	8	13	23	1	7	16	24
General resources	20	23	27	28	29	32	3	12	16	31	3	11	16	30
Microbes	19	31	38	45	53	60	3	12	49	64	2	9	51	62
Mouse and rat	28	32	35	35	36	42	4	17	21	42	4	11	24	39
Other organisms	13	18	21	21	21	22	3	6	13	22	3	4	13	20
Other vertebrates	10	10	10	10	10	11	1	3	7	11	1	3	7	11
Plants	11	16	19	21	25	28	2	10	18	30	2	9	20	31
Worm	9	9	9	9	9	10	1	4	6	11	1	4	8	13
Yeast	11	15	18	18	18	21	2	9	10	21	2	7	12	21
Other molecules
Carbohydrates	5	6	6	6	6	7			7	7			5	5
Compounds				2	6	12		1	14	15		1	15	16
Databases								26		26		25	1	26
Enzymes														2
Metabolites			3	4	7	12		1	12	13		1	13	14
Peptides													1	1
Small molecules	1	3	6	6	9	13		2	13	15		2	15	17
Protein
2D Structure prediction	29	51	58	60	63	65	1		65	66			56	56
3D Structural features		53	70	75	85	100	1	2	103	106	1	2	107	110
3D Structure comparison	78	35	45	50	59	71	1	6	68	75	1	6	62	69
3D Structure prediction	78	48	59	60	70	83	4	1	85	90	2	1	83	86
3D Structure retrieval, viewing	28	45	51	52	56	58	4	7	47	58	3	8	42	53
Annotation and function	26	35	44	47	53	57		5	57	62		5	56	61
Biochemical features	25	37	40	41	46	46	2	2	43	47	2	2	41	45
Databases								116	1	117		115	2	117
Do-it-all tools for protein	6	8	8	13	14	15	3		12	15	3		11	14
Domains and motifs	50	86	112	115	121	124		14	115	129		14	109	123
Identification, presentation and format	12	13	14	14	14	14	1		13	14	1		14	15
Networks & Interactions, pathways, enzymes	48	66	88	94	107	125	3	21	113	137	2	19	113	134
Localization and targeting	19	30	38	38	39	41		3	39	42		3	34	37
Molecular dynamics and docking		19	21	27	34	40	1		44	45	1		48	49
Phylogeny reconstruction	28	36	44	45	53	54	4	5	47	56	4	4	48	56
Protein expression	7	8	8	8	10	10	1	2	7	10	1	2	8	11
Proteomics	21	25	27	33	37	39	3	4	32	39	3	4	26	33
Sequence comparison				7	14	17			18	18			18	18
Sequence data	7	7	8	9	10	10	1	6	3	10	1	5	3	9
Sequence features	14	25	31	33	38	46	2	2	46	50	2	3	47	52
Sequence retrieval	21	27	29	29	31	29	1	6	21	28	1	7	20	28
RNA
Databases							0	24	1	25		23	2	25
Functional RNAs	9	14	19	26	32	37	0	5	39	44		5	41	46
General resources	8	10	10	10	10	11	4	3	4	11	5	2	4	11
Motifs	9	19	21	22	23	25	0	1	26	27		1	25	26
Sequence retrieval	11	11	10	11	11	9	0	2	7	9		2	7	9
Structure prediction, visualization and design	24	38	47	54	58	62	0	3	65	68		3	64	67
Sequence comparison
Alignment editing and visualization	14	20	21	21	23	25	0	0	25	25			23	23
Analysis of aligned sequences	27	43	59	60	62	64	0	0	65	65		1	57	58
Comparative genomics	19	26	33	35	37	48	2	7	40	49	2	6	33	41
Multiple sequence alignments	19	38	50	56	57	65	1	0	67	68	1	1	62	64
Other alignment tools	6	11	11	11	11	12	0	0	13	13			12	12
Pairwise sequence alignments	11	22	23	26	33	35	1	0	34	35	1		30	31
Similarity searching	13	31	47	47	49	50	1	2	49	52	1	3	45	49
Total unique resources, databases and tools in Bioinformatics Links Directory	700+	1000+	1100+	1200+	1400	1500	144	480	1250	1874	134	455	1205	1794

^aA complete listing of all URLs listed in the Nucleic Acids Research 2012 Web Server Issue can be accessed online at: http://bioinformatics.ca/links_directory/narweb2012.