New & Noteworthy
GENETICS Knowledgebase and Database Resources
May 08, 2023
The May 2023 issue of GENETICS features the second annual collection of Model Organism Database articles. Scientists from Alliance of Genome Resources member groups SGD, RGD, ZFIN, Gene Ontology, and Xenbase have provided updates on recent activities and innovations. Be sure to browse the issue and get acquainted with these excellent Knowledgebase and Database Resource papers at GENETICS. Cover art by Vivid Biology.
Categories: Announcements
Tags: Saccharomyces cerevisiae, yeast
Apply Now for the 2023 Yeast Genetics and Genomics Course
March 10, 2023
For over 50 years, the legendary Yeast Genetics & Genomics course has been taught each summer at Cold Spring Harbor Laboratory. (OK, the name didn’t include “Genomics” in the beginning…). The list of people who have taken the course reads like a Who’s Who of yeast research, including Nobel laureates and many of today’s leading scientists.
The application deadline is April 1st, so don’t miss your chance!
Find all the details and application form at the CSHL Meetings & Courses site. This year’s instructors – Grant Brown, Maitreya Dunham, Soni Lacefield, and Greg Lang – have designed a course (July 25 – August 15) that provides a comprehensive education in all things yeast, from classical genetics through up-to-the-minute genomics. Students will perform and interpret experiments, learning about things like:
- Finding and Analyzing Yeast Information Using SGD
- Transformation & genome engineering
- Microscopy
- Manipulating yeast
- Dissecting tetrads
- Isolating mutants
- Working with essential genes
- Synthetic genetic arrays
- Fluctuation assays
- Whole genome sequencing & analysis
- Deep mutational scanning
Techniques have been summarized in the accompanying course manual, published by CSHL Press.
Scientists who aren’t part of large, well-known yeast labs are especially encouraged to apply – for example, professors and instructors who want to incorporate yeast into their undergraduate genetics classrooms; scientists who want to transition from mathematical, computational, or engineering disciplines into bench science; and researchers from small labs or institutions where it would otherwise be difficult to learn the fundamentals of yeast genetics and genomics. Significant stipends (in the 30-50% range of total fees) are available to individuals expressing a need for financial support and who are selected into the course.
Besides its scientific content, the fun and camaraderie at the course is also legendary. In between all the hard work there are late-night chats at the bar and swimming at the beach. There’s a fierce competition between students at the various CSHL courses in the Plate Race, which is a relay in which teams have to carry stacks of 40 Petri dishes (used, of course). There’s also typically a sailboat trip, a microscopy contest, and a mysterious “Dr. Evil” lab!
The Yeast Genetics & Genomics Course is loads of fun – don’t miss out!
Categories: Announcements, Conferences
Apply Now for the 2023 Fungal Pathogen Genomics Course
February 02, 2023
Fungal Pathogen Genomics is an exciting several day long course that provides experimental biologists working on fungal organisms with hands-on experience in genomic-scale data analysis. Through a collaborative teaching effort between the web-based fungal data mining resources FungiDB, EnsemblFungi, PomBase, SGD, CGD, MycoCosm, and JGI, students will learn how to utilize the unique tools provided by each database, develop testable hypotheses, and analyze various ‘omics’ datasets across multiple databases.
Daily activities will include individual and group training exercises, supplementary lectures on bioinformatics techniques and tools used by various databases, and presentations by distinguished guest speakers covering the following topics:
- Comparative genomics, gene trees, whole-genome alignment
- Identification of orthologs and orthology-based inference
- Gene pages and genome browsers
- RNA-Seq analysis and visualization in VEuPathDB Galaxy
- Variant calling analysis and Ensembl Variant Effect Predictor (VEP) tool
- Development of advanced biologically relevant queries using FungiDB ‘search strategies’ and mining integrated datasets (proteomics, transcriptomics, phenotypes, etc.)
- Genetic interactions, virulence genes, secondary metabolites
- Overview of ontology structure, evidence, available tools, slimming and enrichment
- Introduction to manual genome annotation and curation using Apollo, a web-based platform for structural and functional genome annotation (MycoCosm, Ensembl Fungi, FungiDB)
The application deadline for the Fungal Pathogen Genomics workshop to be held May 9-13, 2023 is February 16, 2023.
Don’t miss out – apply now!
Categories: Announcements, Conferences
Happy Holidays from SGD!
December 19, 2022
Stanford University will be closed for two weeks starting Wednesday, December 21, and will reopen on Wednesday, January 4, 2023. SGD staff members will be taking time off, but the website will be up and running throughout the winter break, and we will resume responding to user requests and questions in the new year.
Categories: Announcements
Global Biodata Coalition selects SGD in first set of Global Core Biodata Resources
December 15, 2022
We are proud that SGD has been included in the first list of Global Core Biodata Resources (GCBRs) announced by the Global Biodata Coalition (GBC)! This collection of 37 resources comprises deposition databases which archive and preserve primary research data, and knowledgebases, such as SGD, that add value to research data through expert curation and annotation. The list is meant to highlight those data resources whose long term funding and sustainability is critical to life science and biomedical research worldwide.
GCBRs represent the most crucial resources within the global life science data community. SGD’s selection as a key global data resource recognizes that SGD is essential to the global research endeavor.
For more information regarding the Global Biodata Coalition, including a link to the full list of selected core biodata resources, please see the full press release from the GBC.
Categories: Announcements
Predicted 3D Structures of Yeast Complexes
January 20, 2022
In an exciting new paper, Humphreys et al. describe the use of deep-learning-based algorithms to predict structures of not only single proteins, but assemblies of proteins. The team used rapid RoseTTAFold combined with the more accurate AlphaFold to build structural models for 106 previously unidentified protein assemblies and 806 complexes that had not been structurally characterized. The complexes have up to five subunits and are involved in numerous critical roles in cell biology.
Go look for your own proteins of interest at the ModelArchive and search in the Home page. Also find the link on the resources section of the SGD Interaction and Protein pages.
Categories: Announcements, Data updates, Paper of the Week
Tags: protein complex, Saccharomyces cerevisiae, yeast protein assembly
Protein Complex Page Updates
December 01, 2021
SGD has updated our protein complex pages to have the same format as gene pages, with tabs across the top for each category of information, including a Summary page, a new Gene Ontology page, and a new Literature page for each complex. Just as we do for all of your favorite genes, Gene Ontology and Literature curation for complexes will be ongoing.
If you have any questions or feedback about the updates to our complex pages, please do not hesitate to contact us at any time.
Categories: Announcements, Data updates, Website changes
Tags: protein complex, Saccharomyces cerevisiae
Updates to legacy gene names
November 05, 2021
SGD has long been the keeper of the official Saccharomyces cerevisiae gene nomenclature. Robert Mortimer handed over this responsibility to SGD in 1993 after maintaining the yeast genetic map and gene nomenclature for 30 years.
The accepted format for gene names in S. cerevisiae comprises three uppercase letters followed by a number. The letters typically signify a phrase (referred to as the “Name Description” in SGD) that provides information about a function, mutant phenotype, or process related to that gene, for example “ADE” for “ADEnine biosynthesis” or “CDC” for “Cell Division Cycle”. Gene names for many types of chromosomal features follow this basic format regardless of the type of feature named, whether an ORF, a tRNA, another type of non-coding RNA, an ARS, or a genetic locus. Some S. cerevisiae gene names that pre-date the current nomenclature standards do not conform to this format, such as MRLP38, RPL1A, and OM45.
A few historical gene names predate both the nomenclature standards and the database, and were less computer-friendly than more recent gene names, due to the presence of punctuation. SGD recently updated these gene names to be consistent with current standards and to be more software-friendly by removing punctuation. The old names for these four genes have been retained as aliases.
| ORF | Old gene name | New gene name |
|---|---|---|
| YGL234W | ADE5,7 | ADE57 |
| YER069W | ARG5,6 | ARG56 |
| YBR208C | DUR1,2 | DUR12 |
| YIL154C | IMP2′ | IMP21 |
Categories: Announcements, Data updates
Tags: gene nomenclature
BREWMOR Workshop: Preparing Undergraduate Students for Research Experiences
February 03, 2021
BREWMOR: Bridging Research and Education With Model ORganisms (formerly BREW) will be hosting a virtual workshop titled, “Preparing Undergraduate Students for Research Experiences,” on Friday February 19th, 2021 from 4 – 6:30 PM US Eastern time.
After a very successful virtual BREW (Bridging Research and Education Workshop) in July of 2020 as part of the TAGC meeting, a steering committee was formed to coordinate activities of the BREW community. The name of the community was changed to BREWMOR: Bridging Research and Education With Model ORganisms, to include model organisms beyond yeast.
A micro-BREWMOR event that will be held virtually on Friday February 19th, 2021 from 4-6:30 PM US Eastern time. The main purpose of the event is to provide a forum for social interactions and building a community for support and resource sharing. The theme of this micro-BREWMOR will be “Preparing Undergraduate Students for Research Experiences”. The workshop will include a session related to the event’s main theme and opportunities to connect and collaborate with other undergraduate research mentors and teachers in multiple small breakout rooms focused on various topics.
Please register by February 8th at https://forms.gle/fdBCFxYjWuY38tSG6 . Registration is free.
We hope you can join us at the micro-BREWMOR!
https://brewmor.weebly.com/gatherings.html
Categories: Announcements
Apply Now for the 2021 Fungal Pathogen Genomics (Virtual) Course
January 21, 2021
Fungal Pathogen Genomics is an exciting several day long course that provides experimental biologists working on fungal organisms with hands-on experience in genomic-scale data analysis. Through a collaborative teaching effort between the web-based fungal data mining resources FungiDB, EnsemblFungi, PomBase, SGD, CGD, MycoCosm, and JGI, students will learn how to utilize the unique tools provided by each database, develop testable hypotheses, and analyze various ‘omics’ datasets across multiple databases.
Please note: Due to the ongoing Covid-19 pandemic, the 2021 Fungal Pathogen Genomics course will be delivered in a virtual format.
Daily activities will include individual and group training exercises, supplementary lectures on bioinformatics techniques and tools used by various databases, and presentations by distinguished guest speakers covering the following topics:
- Comparative genomics, gene trees, whole-genome alignment
- Identification of orthologs and orthology-based inference
- Genome browsers and gene pages
- RNA-Seq analysis and visualization in VEuPathDB Galaxy
- Variant calling analysis and Ensembl Variant Effect Predictor (VEP) tool
- Development of advanced biologically relevant queries using FungiDB ‘search strategies’ and mining integrated datasets (proteomics, transcriptomics, phenotypes, etc.)
- Genetic interactions, virulence genes, secondary metabolites
- Overview of ontology structure, evidence, available tools, slimming and enrichment
- Introduction to annotation and curation of fungal genomes (e.g. Apollo in EnsemblFungi, FungiDB, and MycoCosm/JGI)
The application deadline for the Fungal Pathogen Genomics workshop to be held May 10-14, 2021 in virtual format is February 18, 2021.
Don’t miss out – apply now!
Categories: Announcements