WormBase ParaSite is recruiting

We’re looking for a bioinformatician to join the WormBase ParaSite team. If you have an MSc/PhD in bioinformatics (or related), experience working with relational database systems and an interest in genomics, please consider applying! Informal enquiries to parasite-help@sanger.ac.uk are welcome. Closing date 23rd November.

To apply: https://www.embl.de/jobs/searchjobs/index.php?ref=EBI01718

Announcing WormBase ParaSite Release 15

We’re delighted to announce the release of WormBase ParaSite 15, our biggest release yet!

New genomes

This release sees the addition of assemblies of 19 new species:

Genome and annotation updates

We have also incorporated alternative or updated assemblies/gene models for a further 8 species:

  • An alternative (PacBio) assembly from Sun-Yat Sen University for Angiostrongylus cantonensis (PRJNA350391,  Xu et al, 2019).
  • An alternative Hymenolepis diminuta assembly from The University of Warmia and Mazury (PRJEB30942, Nowak et al., 2019).
  • An alternative (PacBio) Steinernema feltiae assembly (PRJNA353610, Fu et al., 2020).
  • An alternative (PacBio) Schistosoma japonicum assembly from Fudan University (PRJNA520774, Luo et al., 2019).
  • Schistosoma haematobium (PRJNA78265) has been updated to reflect an assembly update in INSDC (GCA_000699445.2, Stroehlein et al., 2019). Gene ID mappings from the previous assembly (GCA_000699445.1) are available in the GFF file, and on gene pages.
  • A handful of curated gene models have been added to the Fasciola hepatica (PRJEB25283) annotation, submitted by Emily Robb of Queens’ University Belfast.
  • Curated gene models for the P-glycoprotein repertoire have been added to the Parascaris univalens (PRJNA386823) annotation, submitted by Alexander Gerhard of The Free University of Berlin.
  • The Haemonchus contortus (PRJEB506) annotation has been updated to reflect ongoing curation by Steve Doyle and colleagues at the Wellcome Sanger Institute.

RNAi data

We have imported phenotype data from the recent Schistosoma mansoni RNAi screen by Wang et al., 2020. You can browse the data from S. mansoni gene pages (see the “phenotype” link in the left hand menu). Please let us know if you have any feedback or suggestions for other RNAi studies that you’d like to see in WormBase ParaSite.

Other changes to note

  • The Ancylostoma ceylanicum (PRJNA72583) annotation has been updated to incorporate some missing gene models.
  • Caenorhabditis sp. 34 has been renamed to Caenorhabditis inopinata.
  • In response to feedback from the community, we now present two alternative Steinernema carpocapsae assemblies: GCA_000757645.1, as described by Dillman et al., 2015 and GCA_000757645.3, as described by  Serra et al. (2019). The Serra annotation has been updated to incorporate UTRs, which were omitted in WormBase ParaSite 14. IDs for genes on the X chromosome have also been updated to follow the naming convention of the rest of the gene set. ID mappings between WBPS14 GCA_000757645.3 and WBPS15 GCA_000757645.3 are available on gene pages and in the GFF file. A mapping between gene IDs in GCA_000757645.1 and GCA_000757645.3 is available on the WBPS FTP site.
  • IsoSeq data for the heartworm Dirofilaria immitis is available on JBrowse, submitted by Nic Wheeler and colleagues of the University of Wisconsin-Madison.
  • We have added the alternative Necator americanus gene set, described by Logan et al., 2020, as a JBrowse track.

Alternative gene set for Necator americanus

Logan et al. (2020) have published an alternative set of gene predictions for Necator americanus in PLoS Neglected Tropical Diseases, based on both RNA-seq and proteomics data and generated via the MAKER pipeline.

Their gene predictions can be downloaded from the WormBase ParaSite FTP site at:
ftp://ftp.ebi.ac.uk/pub/databases/wormbase/parasite/datasets/logan_2020_32453752

Thanks to Javier Sotillo Gallego for providing the data!

Parasitic Helminths: New Perspectives in Biology and Infection

30th August – 4th September, 2020: Bratsera Hotel, Hydra, Greece.

Registration: 14 January – 28 February 2020

http://hydra.bio.ed.ac.uk/

The 14th conference in a series previously titled Molecular and Cellular Biology of Helminth Parasites

About the Meeting

The study of helminth parasites continues to excite great interest across the suite of modern scientific themes. With a wealth of genome information and high-throughput technologies, new drug and vaccine development, and intricate host-parasite molecular interactions, we are witnessing a new era of research on these organisms and the diseases they cause. Parasitic Helminths : New Perspectives in Biology and Infection continues the highly successful series now held every year on the beautiful island of Hydra, Greece. All major helminth research areas are covered, including new genomics of animal- and plant-parasitic nematodes, interfaces with free-living helminths such as C. elegans and planarians, developmental and molecular biology, genetics, neurobiology, pharmacology, immunology and vaccine research, all aimed at creating new strategies for control of these prevalent parasitic organisms and the diseases they cause.

Venue

A key feature of the Hydra venue is the Bratsera Hotel hosting the scientific sessions, and the quiet, traffic-free town with ample facilities for informal interactions between delegates. A wide range of accommodation is available close by, including pensions for those on a tight budget. Attendance is limited to 100 people, consistent with a discussion-orientated meeting in which every delegate is an active participant – early registration is encouraged!

Invited Speakers 2020

Keynote Speaker: Jonathan Ewbank, Marseille, France

Confirmed Speakers:

  • Julie Ahringer, Cambridge, UK
  • Adler Dillman, Riverside, USA
  • Sebastian Eves-van den Akker, Cambridge
  • Jennifer Keiser, Basel, Switzerland
  • Frédéric Landmann, Montpellier, France
  • Meera Nair, Riverside, USA
  • Phil Newmark, Madison, USA
  • Meta Roestenberg, Leiden, Netherlands
  • Mark Siracusa, Newark, USA

Organising Committee

  • Amy Buck, University of Edinburgh
  • James Collins, University of Texas
  • Richard E Davis, University of Colorado
  • Kleoniki Gounaris, Imperial College
  • Rick Maizels, University of Glasgow
  • Murray Selkirk, Imperial College

Brugia pahangi material available

The Devaney group have small numbers of adult B. pahangi and larger numbers of Mf available to others for research purposes.  If this would be useful, please contact eileen.devaney@glasgow.ac.uk with approximate numbers, life stage required and whether fresh or frozen material is suitable. The B. pahangi life cycle is funded by a grant from the Wellcome Trust (208390/Z/17/Z).

Helminth Bioinformatics Course in Accra, Ghana: Open for Applications

We’re pleased to announce that a new Wellcome Advanced Course in helminth bioinformatics is now open for applications. The course is aimed at Africa-based researchers at various levels. It will be a hands on and practical introduction to bioinformatics for helminth researchers, covering:

  • The use of public databases (including WormBase ParaSite) to explore gene and protein function
  • Genome assembly
  • Variant calling
  • Differential gene expression
  • Unix/linux command-line and some basic R

Dates and Deadlines

The course will be held at the West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Accra, Ghana, from 8 -13th September 2019.

The course is free to attend for non-commercial applicants, and a number of bursaries are available to cover travel, accommodation and sustenance.

The deadline for applications is 9th May.

More details are available here: https://coursesandconferences.wellcomegenomecampus.org/our-events/helminth-bioinformatics-ghana-2019/

 

 

Parasitic Helminths: New Perspectives in Biology and Infection

1st – 6th September, 2019: Hydra, Greece.

Registration: 13th Jan- 29th March 2019.

http://hydra.bio.ed.ac.uk/

 

Title

 

About the meeting

The study of helminth parasites continues to excite great interest across the suite of modern scientific themes. With a wealth of genome information and high-throughput technologies, new drug and vaccine development, and intricate host-parasite molecular interactions, we are witnessing a new era of research on these organisms and the diseases they cause. Parasitic Helminths: New Perspectives in Biology and Infection will be the 13th in a highly successful series now held every year on the beautiful island of Hydra, Greece. All major helminth research areas are covered, including new genomics of animal- and plant-parasitic nematodes, interfaces with free-living helminths such as C. elegans and planarians, developmental and molecular biology, genetics, neurobiology, pharmacology, immunology and vaccine research, all aimed at creating new strategies for control of these prevalent parasitic organisms and the diseases they cause.

 

Meeting home

Meeting registration

Registration for 2019 will open on Monday January 14 and close on Friday March 29. For questions, please email us at hydra@ed.ac.uk
Attendance is limited to 100 people, consistent with a discussion-orientated meeting in which every delegate is an active participant – early registration is encouraged.

Invited speakers 2019

Keynote Speaker

Alejandro Sánchez Alvarado, USA
Small RNA Mini-Symposium

Confirmed Speakers

Amy Buck, Edinburgh, UK
Louisa Cochella, Vienna, Austria
Alison Elliott, Entebbe, Uganda
Carolina Escobar, Toledo, Spain
Elodie Ghedin, New York, USA
Nicola Harris, Melbourne, Australia
Karl Hoffmann, Aberystwyth UK
P’ng Loke, New York USA
Peter Sarkies, London, UK
William Sullivan, Santa Cruz, USA

Example program (2018)

The Meeting Program is organized primarily from abstracts submitted by participants, a small group of invited speakers, and an invited Keynote Speaker. Many abstracts are selected for short talks and there are two poster sessions. Ample time to interact with participants is available with free time in the afternoons to explore the island and head to the beach.

See 2018 program

Travel to Hydra

Hydra is a small island in the Argo Saronic Gulf, lying off the east coast of the Peloponnese and easily reached by hydrofoil from the Athens port of Piraeus.

Travel information

Accommodations

The meeting is held at the Bratsera Hotel. A wide range of accommodation is available within 5-10 minutes walk of the conference venue, including pensions for those on a tight budget.

Accommodations

Organizing Committee

Dick Davis, University of Colorado
Kleoniki Gounaris, Imperial College
Rick Maizels, University of Glasgow
Murray Selkirk, Imperial College

What would you like to learn about in our BSP workshop?

We’re looking forward to presenting a workshop at the upcoming BSP Spring meeting in Aberystwyth. To help us prepare, we’d love to know what our users would find most useful for us to cover. Please fill in our quick survey (one question only!): https://www.surveymonkey.co.uk/r/8LYF2YW

 

Featured paper: The Echinococcus canadensis (G7) Genome

Tapeworms of the Echinococcus granulosus sensu lato species complex cause the zoonotic disease echinococcosis. Maldonado et al, from the Kamenetzky group at the University of Buenos Aires, have recently reported the genome assembly and annotation of one of the members of this species complex, Echinococcus canadensis (G7 genotype). The genome paper additionally describes a number of comparative analyses between E. canadensis (G7), E. canadensis (G1) and E. multilocularis, based on gene orthology, genome-wide SNP analyses and identification of regulatory features.

Version 1 of the E. canadensis (G7) genome is currently available in WormBase ParaSite, with version 2 becoming available in release 10.