Rodrigo Lopez

Rodrigo Lopez

Head of Web Production - Web production

Rodrigo Lopez joined EMBL-EBI in 1996 as a systems administrator responsible for the deployment of scientific computing and became the External Services Team Leader in 2002. His Web Production team is responsible for the administration of the web infrastructure, development of core software services such as the EBI search engine and EMBL-EBI's job dispatcher, through which many sequence analysis tools run. Many project teams, both externally and within EMBL-EBI, depend on these developments. Rodrigo's team provides institute-wide support and advice on best practises to users. They are heavily involved in the support and in both technical and scientific training of the core software and systems they maintain. 

BSc In Veterinary Medicine, 1984, MSc Molecular Toxicology and Informatics 1987, University of Oslo. At EMBL-EBI since 1995

ORCID iD: 0000-0003-1256-7306

Tel:+44 (0)1223 494 423 / Fax:+44 (0)1223 494 468

Web production

The Web production team, led by Rodrigo Lopez, focuses on three major areas of service: developing and providing platforms for web services; maintaining web infrastructure; and providing robust and secure frameworks for deploying public bioinformatics services. The team maintains and develops the EBI search engine and job dispatcher framework as well as their corresponding SOAP/REST Web Services. Web production also provides access to core services for project management (document management, project documentation and issue tracking, source code control) and user support.

Publications

2014

Activities at the Universal Protein Resource (UniProt).
UniProt Consortium.
Nucleic Acids Res Volume 42 (2014) p.d191-8
DOI: 10.1093/nar/gkt1140

InterProScan 5: genome-scale protein function classification.
Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong SY, Lopez R, Hunter S.
Bioinformatics Volume 30 (2014) p.1236-1240
DOI: 10.1093/bioinformatics/btu031

2013

Analysis Tool Web Services from the EMBL-EBI.
McWilliam H, Li W, Uludag M, Squizzato S, Park YM, Buso N, Cowley AP, Lopez R.
Nucleic Acids Res Volume 41 (2013) p.w597-600
DOI: 10.1093/nar/gkt376

Facing growth in the European Nucleotide Archive.
Cochrane G, Alako B, Amid C, Bower L, Cerdeño-Tárraga A, Cleland I, Gibson R, Goodgame N, Jang M, Kay S, Leinonen R, Lin X, Lopez R, McWilliam H, Oisel A, Pakseresht N, Pallreddy S, Park Y, Plaister S, Radhakrishnan R, Rivière S, Rossello M, Senf A, Silvester N, Smirnov D, Ten Hoopen P, Toribio A, Vaughan D, Zalunin V.
Nucleic Acids Res Volume 41 (2013) p.d30-5
DOI: 10.1093/nar/gks1175

IPD--the Immuno Polymorphism Database.
Robinson J, Halliwell JA, McWilliam H, Lopez R, Marsh SG.
Nucleic Acids Res Volume 41 (2013) p.d1234-40
DOI: 10.1093/nar/gks1140

The IMGT/HLA database.
Robinson J, Halliwell JA, McWilliam H, Lopez R, Parham P, Marsh SG.
Nucleic Acids Res Volume 41 (2013) p.d1222-7
DOI: 10.1093/nar/gks949

The annotation-enriched non-redundant patent sequence databases.
Li W, Kondratowicz B, McWilliam H, Nauche S, Lopez R.
Database (Oxford) Volume 2013 (2013) p.bat005
DOI: 10.1093/database/bat005

EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats.
Ison J, Kalas M, Jonassen I, Bolser D, Uludag M, McWilliam H, Malone J, Lopez R, Pettifer S, Rice P.
Bioinformatics Volume 29 (2013) p.1325-1332
DOI: 10.1093/bioinformatics/btt113

The EBI enzyme portal.
Alcántara R, Onwubiko J, Cao H, Matos Pd, Cham JA, Jacobsen J, Holliday GL, Fischer JD, Rahman SA, Jassal B, Goujon M, Rowland F, Velankar S, López R, Overington JP, Kleywegt GJ, Hermjakob H, O'Donovan C, Martín MJ, Thornton JM, Steinbeck C.
Nucleic Acids Res Volume 41 (2013) p.d773-80
DOI: 10.1093/nar/gks1112

2012

PSI-Search: iterative HOE-reduced profile SSEARCH searching.
Li W, McWilliam H, Goujon M, Cowley A, Lopez R, Pearson WR.
Bioinformatics Volume 28 (2012) p.1650-1651
DOI: 10.1093/bioinformatics/bts240

Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers.
Schneider MV, Walter P, Blatter MC, Watson J, Brazas MD, Rother K, Budd A, Via A, van Gelder CW, Jacob J, Fernandes P, Nyrönen TH, De Las Rivas J, Blicher T, Jimenez RC, Loveland J, McDowall J, Jones P, Vaughan BW, Lopez R, Attwood TK, Brooksbank C.
Brief Bioinform Volume 13 (2012) p.383-389
DOI: 10.1093/bib/bbr064

2011

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.
Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG.
Mol Syst Biol Volume 7 (2011) p.539
DOI: 10.1038/msb.2011.75

Ongoing and future developments at the Universal Protein Resource.
UniProt Consortium.
Nucleic Acids Res Volume 39 (2011) p.d214-9
DOI: 10.1093/nar/gkq1020

UniProt Knowledgebase: a hub of integrated protein data.
Magrane M, Consortium U.
Database (Oxford) Volume 2011 (2011) p.bar009
DOI: 10.1093/database/bar009

The IMGT/HLA database.
Robinson J, Mistry K, McWilliam H, Lopez R, Parham P, Marsh SG.
Nucleic Acids Res Volume 39 (2011) p.d1171-6
DOI: 10.1093/nar/gkq998

2010

Fast and efficient searching of biological data resources--using EB-eye.
Valentin F, Squizzato S, Goujon M, McWilliam H, Paern J, Lopez R.
Brief Bioinform Volume 11 (2010) p.375-384
DOI: 10.1093/bib/bbp065

A new bioinformatics analysis tools framework at EMBL-EBI.
Goujon M, McWilliam H, Li W, Valentin F, Squizzato S, Paern J, Lopez R.
Nucleic Acids Res Volume 38 (2010) p.w695-9
DOI: 10.1093/nar/gkq313

IPD--the Immuno Polymorphism Database.
Robinson J, Mistry K, McWilliam H, Lopez R, Marsh SG.
Nucleic Acids Res Volume 38 (2010) p.d863-9
DOI: 10.1093/nar/gkp879

BioCatalogue: a universal catalogue of web services for the life sciences.
Bhagat J, Tanoh F, Nzuobontane E, Laurent T, Orlowski J, Roos M, Wolstencroft K, Aleksejevs S, Stevens R, Pettifer S, Lopez R, Goble CA.
Nucleic Acids Res Volume 38 (2010) p.w689-94
DOI: 10.1093/nar/gkq394

2009

The IMGT/HLA database.
Robinson J, Waller MJ, Fail SC, McWilliam H, Lopez R, Parham P, Marsh SG.
Nucleic Acids Res Volume 37 (2009) p.d1013-7
DOI: 10.1093/nar/gkn662

Web services at the European Bioinformatics Institute-2009.
McWilliam H, Valentin F, Goujon M, Li W, Narayanasamy M, Martin J, Miyar T, Lopez R.
Nucleic Acids Res Volume 37 (2009) p.w6-10
DOI: 10.1093/nar/gkp302

InterPro: the integrative protein signature database.
Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C.
Nucleic Acids Res Volume 37 (2009) p.d211-5
DOI: 10.1093/nar/gkn785

2008

Data curation + process curation=data integration + science.
Goble C, Stevens R, Hull D, Wolstencroft K, Lopez R.
Brief Bioinform Volume 9 (2008) p.506-517
DOI: 10.1093/bib/bbn034

A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences.
Chica C, Labarga A, Gould CM, López R, Gibson TJ.
BMC Bioinformatics Volume 9 (2008) p.229
DOI: 10.1186/1471-2105-9-229

2007

EMBL Nucleotide Sequence Database in 2006.
Kulikova T, Akhtar R, Aldebert P, Althorpe N, Andersson M, Baldwin A, Bates K, Bhattacharyya S, Bower L, Browne P, Castro M, Cochrane G, Duggan K, Eberhardt R, Faruque N, Hoad G, Kanz C, Lee C, Leinonen R, Lin Q, Lombard V, Lopez R, Lorenc D, McWilliam H, Mukherjee G, Nardone F, Pastor MP, Plaister S, Sobhany S, Stoehr P, Vaughan R, Wu D, Zhu W, Apweiler R.
Nucleic Acids Res Volume 35 (2007) p.d16-20
DOI: 10.1093/nar/gkl913

Web services at the European bioinformatics institute.
Labarga A, Valentin F, Anderson M, Lopez R.
Nucleic Acids Res Volume 35 (2007) p.w6-11
DOI: 10.1093/nar/gkm291

New developments in the InterPro database.
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, Courcelle E, Das U, Daugherty L, Dibley M, Finn R, Fleischmann W, Gough J, Haft D, Hulo N, Hunter S, Kahn D, Kanapin A, Kejariwal A, Labarga A, Langendijk-Genevaux PS, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Nikolskaya AN, Orchard S, Orengo C, Petryszak R, Selengut JD, Sigrist CJ, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C.
Nucleic Acids Res Volume 35 (2007) p.d224-8
DOI: 10.1093/nar/gkl841

Clustal W and Clustal X version 2.0.
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG.
Bioinformatics Volume 23 (2007) p.2947-2948
DOI: 10.1093/bioinformatics/btm404

2006

The Universal Protein Resource (UniProt): an expanding universe of protein information.
Wu CH, Apweiler R, Bairoch A, Natale DA, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Mazumder R, O'Donovan C, Redaschi N, Suzek B.
Nucleic Acids Res Volume 34 (2006) p.d187-91
DOI: 10.1093/nar/gkj161

EMBL Nucleotide Sequence Database: developments in 2005.
Cochrane G, Aldebert P, Althorpe N, Andersson M, Baker W, Baldwin A, Bates K, Bhattacharyya S, Browne P, van den Broek A, Castro M, Duggan K, Eberhardt R, Faruque N, Gamble J, Kanz C, Kulikova T, Lee C, Leinonen R, Lin Q, Lombard V, Lopez R, McHale M, McWilliam H, Mukherjee G, Nardone F, Pastor MP, Sobhany S, Stoehr P, Tzouvara K, Vaughan R, Wu D, Zhu W, Apweiler R.
Nucleic Acids Res Volume 34 (2006) p.d10-5
DOI: 10.1093/nar/gkj130

2005

InterProScan: protein domains identifier.
Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R.
Nucleic Acids Res Volume 33 (2005) p.w116-20
DOI: 10.1093/nar/gki442

SOAP-based services provided by the European Bioinformatics Institute.
Pillai S, Silventoinen V, Kallio K, Senger M, Sobhany S, Tate J, Velankar S, Golovin A, Henrick K, Rice P, Stoehr P, Lopez R.
Nucleic Acids Res Volume 33 (2005) p.w25-8
DOI: 10.1093/nar/gki491

The Universal Protein Resource (UniProt).
Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS.
Nucleic Acids Res Volume 33 (2005) p.d154-9
DOI: 10.1093/nar/gki070

InterPro, progress and status in 2005.
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L, Copley R, Courcelle E, Das U, Durbin R, Fleischmann W, Gough J, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McDowall J, Mitchell A, Nikolskaya AN, Orchard S, Pagni M, Ponting CP, Quevillon E, Selengut J, Sigrist CJ, Silventoinen V, Studholme DJ, Vaughan R, Wu CH.
Nucleic Acids Res Volume 33 (2005) p.d201-5
DOI: 10.1093/nar/gki106

2004

The EMBL Nucleotide Sequence Database.
Kulikova T, Aldebert P, Althorpe N, Baker W, Bates K, Browne P, van den Broek A, Cochrane G, Duggan K, Eberhardt R, Faruque N, Garcia-Pastor M, Harte N, Kanz C, Leinonen R, Lin Q, Lombard V, Lopez R, Mancuso R, McHale M, Nardone F, Silventoinen V, Stoehr P, Stoesser G, Tuli MA, Tzouvara K, Vaughan R, Wu D, Zhu W, Apweiler R.
Nucleic Acids Res Volume 32 (2004) p.d27-30
DOI: 10.1093/nar/gkh120

The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology.
Camon E, Magrane M, Barrell D, Lee V, Dimmer E, Maslen J, Binns D, Harte N, Lopez R, Apweiler R.
Nucleic Acids Res Volume 32 (2004) p.d262-6
DOI: 10.1093/nar/gkh021

UniProt archive.
Leinonen R, Diez FG, Binns D, Fleischmann W, Lopez R, Apweiler R.
Bioinformatics Volume 20 (2004) p.3236-3237
DOI: 10.1093/bioinformatics/bth191

UniProt: the Universal Protein knowledgebase.
Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS.
Nucleic Acids Res Volume 32 (2004) p.d115-9
DOI: 10.1093/nar/gkh131

2003

WU-Blast2 server at the European Bioinformatics Institute.
Lopez R, Silventoinen V, Robinson S, Kibria A, Gish W.
Nucleic Acids Res Volume 31 (2003) p.3795-3798
DOI: 10.1093/nar/gkg573

The European Bioinformatics Institute web site: a new view.
Lopez R, Robinson S, Kibria A, Harte N, Patel G, Harper R, Quevillon E, Silventoinen V, Kallio K, Jokinen P.
Bioinformatics Volume 19 (2003) p.546-547
DOI: 10.1093/bioinformatics/btg022

The EMBL Nucleotide Sequence Database: major new developments.
Stoesser G, Baker W, van den Broek A, Garcia-Pastor M, Kanz C, Kulikova T, Leinonen R, Lin Q, Lombard V, Lopez R, Mancuso R, Nardone F, Stoehr P, Tuli MA, Tzouvara K, Vaughan R.
Nucleic Acids Res Volume 31 (2003) p.17-22
DOI: 10.1093/nar/gkg021

2002

The EBI SRS server-new features.
Zdobnov EM, Lopez R, Apweiler R, Etzold T.
Bioinformatics Volume 18 (2002) p.1149-1150
DOI: 10.1093/bioinformatics/18.8.1149

The EMBL Nucleotide Sequence Database.
Stoesser G, Baker W, van den Broek A, Camon E, Garcia-Pastor M, Kanz C, Kulikova T, Leinonen R, Lin Q, Lombard V, Lopez R, Redaschi N, Stoehr P, Tuli MA, Tzouvara K, Vaughan R.
Nucleic Acids Res Volume 30 (2002) p.21-26
DOI: 10.1093/nar/30.1.21

The EBI SRS server--recent developments.
Zdobnov EM, Lopez R, Apweiler R, Etzold T.
Bioinformatics Volume 18 (2002) p.368-373
DOI: 10.1093/bioinformatics/18.2.368

2001

The InterPro database, an integrated documentation resource for protein families, domains and functional sites.
Apweiler R, Attwood TK, Bairoch A, Bateman A, Birney E, Biswas M, Bucher P, Cerutti L, Corpet F, Croning MD, Durbin R, Falquet L, Fleischmann W, Gouzy J, Hermjakob H, Hulo N, Jonassen I, Kahn D, Kanapin A, Karavidopoulou Y, Lopez R, Marx B, Mulder NJ, Oinn TM, Pagni M, Servant F, Sigrist CJ, Zdobnov EM.
Nucleic Acids Res Volume 29 (2001) p.37-40
DOI: 10.1093/nar/29.1.37

The EMBL nucleotide sequence database.
Stoesser G, Baker W, van den Broek A, Camon E, Garcia-Pastor M, Kanz C, Kulikova T, Lombard V, Lopez R, Parkinson H, Redaschi N, Sterk P, Stoehr P, Tuli MA.
Nucleic Acids Res Volume 29 (2001) p.17-21
DOI: 10.1093/nar/29.1.17

2000

The EMBL nucleotide sequence database.
Baker W, van den Broek A, Camon E, Hingamp P, Sterk P, Stoesser G, Tuli MA.
Nucleic Acids Res Volume 28 (2000) p.19-23
DOI: 10.1093/nar/28.1.19

1999

The EMBL Nucleotide Sequence Database.
Stoesser G, Tuli MA, Lopez R, Sterk P.
Nucleic Acids Res Volume 27 (1999) p.18-24
DOI: 10.1093/nar/27.1.18

1994

Evaluation of the exon predictions of the GRAIL software.
Lopez R, Larsen F, Prydz H.
Genomics Volume 24 (1994) p.133-136
DOI: 10.1006/geno.1994.1590

1992

Database contamination.
Lopez R, Kristensen T, Prydz H.
Nature Volume 355 (1992) p.211
DOI: 10.1038/355211a0

A type-III DNA restriction and modification system in Bacillus cereus?
Hegna IK, Karlstrøm ES, Lopez R, Kristensen T, Kolstø AB.
Gene Volume 114 (1992) p.149-150
DOI: 10.1016/0378-1119(92)90722-2

Cloning of a gene from Bacillus cereus with homology to the mreB gene from Escherichia coli.
Narahara A, Naterstad K, Kristensen T, Lopez R, Bork P, Kolstø AB.
Gene Volume 122 (1992) p.181-185
DOI: 10.1016/0378-1119(92)90047-s

CpG islands as gene markers in the human genome.
Larsen F, Gundersen G, Lopez R, Prydz H.
Genomics Volume 13 (1992) p.1095-1107
DOI: 10.1016/0888-7543(92)90024-m

Team members

Simone Federico Maria Badoer
Nicola Buso
Andrew Cowley
Andrea Cristofori
Tamer Gur
Philip Lewis
Weizhong Li
Hamish McWilliam
Youngmi Park
Silvano Squizzato
Mahmut Uludag
Kelly Walsh