The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024

被引：210
作者：
Madeira, Fabio [1 ]
Madhusoodanan, Nandana [1 ]
Lee, Joonheung [1 ]
Eusebi, Alberto [1 ]
Niewielska, Ania [1 ]
Tivey, Adrian R. N. [1 ]
Lopez, Rodrigo [1 ]
Butcher, Sarah [1 ]
机构：
[1] Wellcome Trust Genome Campus, European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Hinxton CB10 1SD, England
来源：
NUCLEIC ACIDS RESEARCH | 2024年 / 52卷 / W1期
关键词：
D O I：
10.1093/nar/gkae241
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
The EMBL-EBI Job Dispatcher sequence analysis tools framework (https://www.ebi.ac.uk/jdispatcher) enables the scientific community to perform a diverse range of sequence analyses using popular bioinformatics applications. Free access to the tools and required sequence datasets is provided through user-friendly web applications, as well as via RESTful and SOAP-based APIs. These are integrated into popular EMBL-EBI resources such as UniProt, InterPro, ENA and Ensembl Genomes. This paper overviews recent improvements to Job Dispatcher, including its brand new website and documentation, enhanced visualisations, improved job management, and a rising trend of user reliance on the service from low- and middle-income regions. Graphical Abstract
引用
收藏
页码：W521 / W525
页数：5
相关论文
共 21 条
  • [1] PDBe: improved findability of macromolecular structure data in the PDB
    Armstrong, David R.
    Berrisford, John M.
    Conroy, Matthew J.
    Gutmanas, Aleksandras
    Anyango, Stephen
    Choudhary, Preeti
    Clark, Alice R.
    Dana, Jose M.
    Deshpande, Mandar
    Dunlop, Roisin
    Gane, Paul
    Gaborova, Romana
    Gupta, Deepti
    Haslam, Pauline
    Koca, Jaroslav
    Mak, Lora
    Mir, Saqib
    Mukhopadhyay, Abhik
    Nadzirin, Nurul
    Nair, Sreenath
    Paysan-Lafosse, Typhaine
    Pravda, Lukas
    Sehnal, David
    Salih, Osman
    Smart, Oliver
    Tolchard, James
    Varadi, Mihaly
    Svobodova-Varekova, Radka
    Zaki, Hossam
    Kleywegt, Gerard J.
    Velankar, Sameer
    [J]. NUCLEIC ACIDS RESEARCH, 2020, 48 (D1) : D335 - D343
  • [2] UniProt: the Universal Protein Knowledgebase in 2023
    Bateman, Alex
    Martin, Maria-Jesus
    Orchard, Sandra
    Magrane, Michele
    Ahmad, Shadab
    Alpi, Emanuele
    Bowler-Barnett, Emily H.
    Britto, Ramona
    Cukura, Austra
    Denny, Paul
    Dogan, Tunca
    Ebenezer, ThankGod
    Fan, Jun
    Garmiri, Penelope
    Gonzales, Leonardo Jose da Costa
    Hatton-Ellis, Emma
    Hussein, Abdulrahman
    Ignatchenko, Alexandr
    Insana, Giuseppe
    Ishtiaq, Rizwan
    Joshi, Vishal
    Jyothi, Dushyanth
    Kandasaamy, Swaathi
    Lock, Antonia
    Luciani, Aurelien
    Lugaric, Marija
    Luo, Jie
    Lussi, Yvonne
    MacDougall, Alistair
    Madeira, Fabio
    Mahmoudy, Mahdi
    Mishra, Alok
    Moulang, Katie
    Nightingale, Andrew
    Pundir, Sangya
    Qi, Guoying
    Raj, Shriya
    Raposo, Pedro
    Rice, Daniel L.
    Saidi, Rabie
    Santos, Rafael
    Speretta, Elena
    Stephenson, James
    Totoo, Prabhat
    Turner, Edward
    Tyagi, Nidhi
    Vasudev, Preethi
    Warner, Kate
    Watkins, Xavier
    Zellner, Hermann
    [J]. NUCLEIC ACIDS RESEARCH, 2023, 51 (D1) : D523 - D531
  • [3] BLAST plus : architecture and applications
    Camacho, Christiam
    Coulouris, George
    Avagyan, Vahram
    Ma, Ning
    Papadopoulos, Jason
    Bealer, Kevin
    Madden, Thomas L.
    [J]. BMC BIOINFORMATICS, 2009, 10
  • [4] The European Nucleotide Archive in 2021
    Cummins, Carla
    Ahamed, Alisha
    Aslam, Raheela
    Burgin, Josephine
    Devraj, Rajkumar
    Edbali, Ossama
    Gupta, Dipayan
    Harrison, Peter W.
    Haseeb, Muhammad
    Holt, Sam
    Ibrahim, Talal
    Ivanov, Eugene
    Jayathilaka, Suran
    Kadhirvelu, Vishnukumar
    Kay, Simon
    Kumar, Manish
    Lathi, Ankur
    Leinonen, Rasko
    Madeira, Fabio
    Madhusoodanan, Nandana
    Mansurova, Milena
    O'Cathail, Colman
    Pearce, Matt
    Pesant, Stephane
    Rahman, Nadim
    Rajan, Jeena
    Rinck, Gabriele
    Selvakumar, Sandeep
    Sokolov, Alexey
    Suman, Swati
    Thorne, Ross
    Totoo, Prabhat
    Vijayaraja, Senthilnathan
    Waheed, Zahra
    Zyoud, Ahmad
    Lopez, Rodrigo
    Burdett, Tony
    Cochrane, Guy
    [J]. NUCLEIC ACIDS RESEARCH, 2022, 50 (D1) : D106 - D110
  • [5] Nextflow enables reproducible computational workflows
    Di Tommaso, Paolo
    Chatzou, Maria
    Floden, Evan W.
    Prieto Barja, Pablo
    Palumbo, Emilio
    Notredame, Cedric
    [J]. NATURE BIOTECHNOLOGY, 2017, 35 (04) : 316 - 319
  • [6] Eddy Sean R, 2009, Genome Inform, V23, P205
  • [7] Ensembl 2024
    Harrison, Peter W.
    Amode, M. Ridwan
    Austine-Orimoloye, Olanrewaju
    Azov, Andrey G.
    Barba, Matthieu
    Barnes, If
    Becker, Arne
    Bennett, Ruth
    Berry, Andrew
    Bhai, Jyothish
    Bhurji, Simarpreet Kaur
    Boddu, Sanjay
    Lins, Paulo R. Branco
    Brooks, Lucy
    Ramaraju, Shashank Budhanuru
    Campbell, Lahcen, I
    Martinez, Manuel Carbajo
    Charkhchi, Mehrnaz
    Chougule, Kapeel
    Cockburn, Alexander
    Davidson, Claire
    De Silva, Nishadi H.
    Dodiya, Kamalkumar
    Donaldson, Sarah
    El Houdaigui, Bilal
    El Naboulsi, Tamara
    Fatima, Reham
    Giron, Carlos Garcia
    Genez, Thiago
    Grigoriadis, Dionysios
    Ghattaoraya, Gurpreet S.
    Martinez, Jose Gonzalez
    Gurbich, Tatiana A.
    Hardy, Matthew
    Hollis, Zoe
    Hourlier, Thibaut
    Hunt, Toby
    Kay, Mike
    Kaykala, Vinay
    Le, Tuan
    Lemos, Diana
    Lodha, Disha
    Marques-Coelho, Diego
    Maslen, Gareth
    Merino, Gabriela Alejandra
    Mirabueno, Louisse Paola
    Mushtaq, Aleena
    Hossain, Syed Nakib
    Ogeh, Denye N.
    Sakthivel, Manoj Pandian
    [J]. NUCLEIC ACIDS RESEARCH, 2023, : D891 - D899
  • [8] WormBase ParaSite - a comprehensive resource for helminth genomics
    Howe, Kevin L.
    Bolt, Bruce J.
    Shafie, Myriam
    Kersey, Paul
    Berriman, Matthew
    [J]. MOLECULAR AND BIOCHEMICAL PARASITOLOGY, 2017, 215 : 2 - 10
  • [9] Tools and data services registry: a community effort to document bioinformatics resources
    Ison, Jon
    Rapacki, Kristoffer
    Menager, Herve
    Kalas, Matus
    Rydza, Emil
    Chmura, Piotr
    Anthon, Christian
    Beard, Niall
    Berka, Karel
    Bolser, Dan
    Booth, Tim
    Bretaudeau, Anthony
    Brezovsky, Jan
    Casadio, Rita
    Cesareni, Gianni
    Coppens, Frederik
    Cornell, Michael
    Cuccuru, Gianmauro
    Davidsen, Kristian
    Della Vedova, Gianluca
    Dogan, Tunca
    Doppelt-Azeroual, Olivia
    Emery, Laura
    Gasteiger, Elisabeth
    Gatter, Thomas
    Goldberg, Tatyana
    Grosjean, Marie
    Gruening, Bjoern
    Helmer-Citterich, Manuela
    Ienasescu, Hans
    Ioannidis, Vassilios
    Jespersen, Martin Closter
    Jimenez, Rafael
    Juty, Nick
    Juvan, Peter
    Koch, Maximilian
    Laibe, Camille
    Li, Jing-Woei
    Licata, Luana
    Mareuil, Fabien
    Micetic, Ivan
    Friborg, Rune Mollegaard
    Moretti, Sebastien
    Morris, Chris
    Moeller, Steffen
    Nenadic, Aleksandra
    Peterson, Hedi
    Profiti, Giuseppe
    Rice, Peter
    Romano, Paolo
    [J]. NUCLEIC ACIDS RESEARCH, 2016, 44 (D1) : D38 - D47
  • [10] InterProScan 5: genome-scale protein function classification
    Jones, Philip
    Binns, David
    Chang, Hsin-Yu
    Fraser, Matthew
    Li, Weizhong
    McAnulla, Craig
    McWilliam, Hamish
    Maslen, John
    Mitchell, Alex
    Nuka, Gift
    Pesseat, Sebastien
    Quinn, Antony F.
    Sangrador-Vegas, Amaia
    Scheremetjew, Maxim
    Yong, Siew-Yit
    Lopez, Rodrigo
    Hunter, Sarah
    [J]. BIOINFORMATICS, 2014, 30 (09) : 1236 - 1240
123