New & Noteworthy
Deadline extended to April 22 for the 2024 Yeast Genetics and Genomics Course
April 09, 2024
The application deadline for the 2024 Yeast Genetics and Genomics Course has been extended to April 22 – don’t miss your chance! Significant financial aid may be available for trainees applying, covering up to 50% of the cost of the course!
Find all the details and application form at the CSHL Meetings & Courses site.
For over 50 years, the legendary Yeast Genetics & Genomics course has been taught each summer at Cold Spring Harbor Laboratory, though 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.
This year’s instructors – Grant Brown, Soni Lacefield, and Greg Lang – have designed a course (July 23 – August 13) 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:
- Transformation & Genome Engineering
- Microscopy
- Manipulating Yeast
- Dissecting Tetrads
- Isolating Mutants
- Working with Essential Genes
- Synthetic Genetic Arrays
- Fluctuation Assays
- Whole Genome Sequencing & Analysis
- QTLMapping
Techniques have been summarized in the accompanying course manual, published by CSHL Press.
Who should attend? 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.
What else goes on there? 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: Conferences
Tags: dna, genetics, genomics, science
New user interface for YeastMine
April 04, 2024
Here at SGD we provide high-quality curated genomic, genetic, and molecular information on the genes and gene products of the budding yeast Saccharomyces cerevisiae. Twelve years ago, in order to accommodate the increasingly complex and diverse needs of researchers for searching and comparing data, SGD implemented InterMine, an open source data warehouse system with a sophisticated querying interface, to create YeastMine.
Today’s news is that we have updated YeastMine to use the new BlueGenes user interface from InterMine. The new interface provides the same functionality you’re already familiar with, wrapped in a new design offering a more interactive experience for exploring and analyzing your data. We are making this switch because AllianceMine at the Alliance of Genome Resources, of which SGD is a founding member, is using the updated interface as well.
YeastMine is a multifaceted search and retrieval environment that provides access to diverse data types. Searches can be initiated with a list of genes, a list of Gene Ontology terms, or lists of many other data types. The results from queries can be combined for further analysis and saved or downloaded in customizable file formats. Queries themselves can be customized by modifying predefined templates or by creating a new template to access a combination of specific data types.
User documentation for the new YeastMine interface is available from InterMine.
Categories: Announcements
Tags: user-interface
Changes to Saccharomyces cerevisiae GFF3 file
March 01, 2024
The saccharomyces_cerevisiae.gff contains sequence features of Saccharomyces cerevisiae and related information such as Locus descriptions and GO annotations. It is fully compatible with Generic Feature Format Version 3. It is updated weekly.
After November 2020, SGD updated the transcripts in the GFF file to reflect the experimentally determined transcripts (Pelechano et al. 2013, Ng et al. 2020), when possible. The longest transcripts were determined for two different growth media – galactose and dextrose. When available, experimentally determined transcripts for one or both conditions were added for a gene. When this data was absent, transcripts matching the start and stop coordinates of an open reading frame (ORF) were used.
Beginning in February 2024, SGD increased the start and stop coordinates of genes to encompass the start and stop coordinates of the longest experimentally determined transcripts, regardless of condition. This change was made in order to comply with JBrowse 2, a newer and more extensible genome browser, which requires that parent features in GFF files (genes) are larger than child features (mRNA, CDS, etc) (Diesh et al., 2023).
This is a standard format used by many groups. SGD uses the GFF file to load the reference tracks in SGD’s genome browser resource.
Categories: Announcements, Data updates
Tags: biology, blog, genetics, news, Saccharomyces cerevisiae
Apply Now for the 2024 Yeast Genetics and Genomics Course
February 13, 2024
For over 50 years, the legendary Yeast Genetics & Genomics course has been taught each summer at Cold Spring Harbor Laboratory, though 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 March 31st, 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, Soni Lacefield, and Greg Lang – have designed a course (July 23 – August 13) 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:
- Transformation & Genome Engineering
- Microscopy
- Manipulating Yeast
- Dissecting Tetrads
- Isolating Mutants
- Working with Essential Genes
- Synthetic Genetic Arrays
- Fluctuation Assays
- Whole Genome Sequencing & Analysis
- QTLMapping
Techniques have been summarized in the accompanying course manual, published by CSHL Press.
Who should attend? 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.
What else goes on there? 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: Conferences