Joint Genome Institute – Metagenomics workshop & 10th Annual Meeting

Announcement from the Joint Genome Institute Mailing list:

February 9 – 13, 2015

The U.S. Department of Energy Joint Genome Institute is offering a five-day workshop on Microbial Genomics and Metagenomics (MGM). The MGM Workshop include seminars and extensive hands-on tutorials on how to use the IMG family of systems for comparative analysis of isolate genomes and metagenomes. Our goal is to provide you with training in microbial genomic and metagenomic analysis and demonstrate how the cutting-edge science and technology of DOE JGI can enhance your research. For more information and to register, click here. Attendance is limited, so act now!

March 24 – 26, 2015

The DOE Joint Genome Institute’s 10th Annual Genomics of Energy & Environment Meeting registration is open.  See the current roster of speakers and register now for the March 24-26, 2015 event. Check out and register for the workshops too.

Once you’ve registered, please submit poster abstracts (from which short talks will be selected). Guidance for abstracts and posters can be found here.

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Wrap-up post – “Ecometagenomics” Symposium at BES/SFE meeting

Thanks to everyone who attended our Symposium at the Joint British/French Ecological Society Meeting last week in Lille, France –  “Accelerating ecology and biodiversity research via ecometagenomics: species, communities and environmental DNA”. A collection of Tweets from this session is now available here on Storify.

We had a great turnout for the meeting session, followed by a hugely successful wine & cheese social sponsored in conjunction with the BES Plants, Soils, and Ecosystems Special Interest Group. And of course we managed to find plenty of holiday cheer walking around the streets of Lille!

2014-12-10 19.45.00

Simon, Dorota, Holly and Serita (left to right), on their way to the wine & cheese social!

 

Moore Foundation EOI call – Marine Microeukaryotes as Experimental Model Systems

Request for Expressions of Interest: Increasing the Potential of Marine Microeukaryotes as Experimental Model Systems through the Development of Genetic Tools

The Marine Microbiology Initiative (MMI) at the Gordon and Betty Moore Foundation aims to enable scientists to uncover the principles that govern the interactions among microbes and that influence nutrient flow in the marine environment. MMI is targeting closing gaps in and supporting the advancement of experimental model systems in microbial oceanography to enable new ways to uncover fundamental biological mechanisms.

We are soliciting expressions of interest (EOIs) for early-stage research projects to develop methods to genetically manipulate marine microeukaryotes as a first step in breaking current bottlenecks in the advancement of experimental model systems. MMI has two primary foci for this expression of interest:

  1. Development of genetic tools for diatoms. Diatoms are key players in the world’s oceans, generating ~20% of the world’s organic carbon, and a strong community of researchers is in place suggesting broad use of successfully developed methods. We are specifically interested in projects to develop reverse and/or forward genetics.
  2. Screening laboratory-scale culture collections for transformable marine microeukaryotes.
    MMI will also consider projects to develop genetic tools and methods with other microeukaryotes that show promise for expanding the way the field can test hypotheses. If your idea does not fit category 1 or 2 above, please contact us prior to submitting your EOI.

MMI encourages EOIs from “inter-organismal” teams of researchers – i.e., complementary groups that have experience in a well-established model system and with a microeukaryote that is not currently genetically tractable – whose collaborative effort will bring innovative approaches to the field.

MMI invites you to send an expression of interest via email that briefly outlines a research project (one paragraph or less), using the following template:

  1. The lead researcher’s name, institution, and expertise.
  2. Indication of focus on genetic tools for diatoms (category 1 above) or laboratory culture screening for
    transformability (category 2 above).
  3. For category 1, the name of the organism(s); or, for category 2, the taxonomic group(s) to be screened.
  4. A methodological or technical challenge that is hindering the development of a genetically
    manipulable marine microeukaryotic system that is ripe for solving and how you would address this
    challenge (3-5 sentences).
  5. The research team that would tackle this challenge, and why each team member’s expertise is relevant
    (one sentence per team member; please include institutional affiliations).

The opportunities that best align with MMI’s strategies and goals will be invited to submit proposals. MMI has allocated $7–10M to support this effort and anticipates making multiple, 2–3 year awards beginning in mid- 2015.

Please submit your EOI by Tuesday January 6, 2015 to Samantha Forde at samantha.forde@moore.org.

NSF Genealogy of Life (GoLife) – 2015 call for proposals

NSF has once again issued its RFP for the Genealogy of Life (GoLife) program. Full proposal deadline is March 25, 2015.

Program Synopsis (from NSF website): 

Comprehensive understanding of life and how and why it changes over time depends on knowledge of the phylogeny (evolutionary relationships) of living and extinct organisms. The goals of the Genealogy of Life (GoLife) program are to resolve the phylogenetic history of all life’s diverse forms and to integrate this genealogical architecture with underlying organismal and environmental data.

The ultimate vision of this program is an open access, comprehensive Genealogy of Life that will provide the comparative framework necessary for testing questions in systematics, evolutionary biology, ecology, and other fields. Strategic integration of this genealogy of life with data layers from genomic, phenotypic, spatial, ecological and temporal data will produce an extensive synthesis of biodiversity and evolutionary sciences. The resulting knowledge infrastructure will enable synthetic research on biological dynamics throughout the history of life on Earth, within current ecosystems, and for predictive modeling of the future evolution of life.

Projects submitted to this program should emphasize increased efficiency in contributing to a complete Genealogy of Life and strategic integration of various types of organismal and environmental data with phylogenies.

This program also seeks to broadly train next generation, integrative phylogenetic biologists, creating the human resource infrastructure and workforce needed to tackle emerging research questions in comparative biology. Projects should train students for diverse careers by exposing them to the multidisciplinary areas of research within the proposal.

Detailed Program Description (from NSF website):

The Genealogy of Life program has four main goals: 1) Taxonomic completeness — containing all described species of a given clade, including those lineages that are extinct, 2) Data completeness —including diverse underlying data layers (e.g., digitized images, specimen collection information, environmental and habitat data, geographic and stratigraphic distributions, genomic and phenomic data, developmental data and ontologies), 3) Dynamic and open structure — allowing the automatic incorporation of new data and taxa, and mechanisms for accessibility to the broad scientific and non-scientific communities, and 4) Training of the next generation of phylogenetic biologists –– integrative training in diverse fields across comparative evolutionary biology. Successful projects will describe how research and training activities will achieve these four overarching goals.

All successful proposals will have the goal of massively increasing the taxonomic and character data space that contributes to making our understanding of life’s genealogy as thorough as possible. When preparing a GoLife proposal, proposers are required to justify the need for phylogenetic analysis on their chosen taxonomic group of study and their approach to advancing data inclusiveness. Taxonomic completeness, as described above in Goal 1, will likely be group-dependent. For example, work on clades that include a rich fossil record should include the fossil taxa in the proposed research. Completeness for other clades will likely be defined differently.

Proposals should focus on poorly sampled clades or data layers within the Genealogy of Life where new data will have a profound impact on new understanding of the pattern of life’s evolution. In accordance with Goal 2 above, justification of data layers to be added is expected to be strategic and to enable future hypothesis-based research. Chosen data layers are likely to be clade-specific. For example, some vertebrate, invertebrate and plant clades will enable approaches that add substantial phenotypic, geochronological, environmental, spatial, and other types of data layers; some prokaryotic clades will enable approaches that add metabolic pathway, genomic and environmental data layers. GoLife proposals should outline the specific types of novel, hypothesis-driven research that would be enabled by the specific phylogenetic and data layer choices that are proposed.

For this year’s solicitation, along with the generation of new phylogenetic data and phylogenetic analyses, GoLife research projects must integrate at least two different data types. Proposals that do not integrate at least two data layers will be returned without review.

Examples of data layers (not an exhaustive list) that could be integrated in GoLife proposals include:

  • a) Genomic/Phylogenomic sequence data
  • b) Genotype-phenotype linkage and mapping
  • c) Morphological data
  • d) Fossil data
  • e) Geochronological data
  • f) Developmental data
  • g) Ontologies
  • h) Geospatial data
  • i) Environmental data
  • j) Digitized voucher specimens
  • k) Encyclopedia of Life webpages
  • l) Behavioral data
  • m) Physiological data
  • n) Metabolic pathways

Length and size of award will depend upon the number and size of the data sets to be added to the Genealogy of Life. Priority will be given to those proposals that provide: 1) the most substantial increase in volume of tree space added, and/or 2) the most significant increase in annotated organismal and environmental data layers. The phylogenetic scope of a GoLife proposal should vastly exceed that of a typical Phylogenetic Systematics core program proposal. Given advances in the field, the size and scope of GoLife proposals should also vastly exceed that of AToL projects.

GoLife projects should leverage existing infrastructure when possible, to avoid redundancy in tools available for comparative biology. Examples of existing infrastructure that GoLife projects could build upon, or access digital data from, include iDigBio, Genbank, Open Tree of Life, etc.

Projects that largely repeat or replicate existing work will not be funded. Additional examples of projects that will not be considered by this program include: 1) projects that only use a single data type (e.g. genomic/phylogenomic or morphological), 2) projects that consist of species surveys, inventories, or descriptions (e.g., Biodiversity: Discovery and Analysis projects), 3) projects that are focused on revisionary systematics (e.g. Advancing Revisionary and Taxonomy and Systematics projects), 4) projects that aim to test a particular hypothesis related to the evolution of a particular group (e.g., Phylogenetic Systematics projects), and 5) projects that are solely focused on the development of new methods or technologies without the generation of substantial amounts of new phylogenetic data. Research proposals that do not focus on poorly sampled clades or data layers within the Genealogy of Life should be submitted to other relevant NSF programs.

Upcoming Ecometagenomics Symposium at the 2014 Joint British/French Ecological Society Meeting

We’ve just finalized details for an upcoming RCN-sponsored symposium at the Joint 2014 Annual Meeting of the British Ecological Society and Société Française d’Ecologie, to be held December 9-12, 2014 at the Grand Palais in Lille, France. Early bird registration is open until October 13th, so don’t delay if you’re interested in coming along!

Symposium Title: Accelerating ecology and biodiversity research via ecometagenomics: species, communities and environmental DNA.

Our confirmed list of speakers is as follows:

  • Pierre Taberlet, Centre National de la Recherche Scientifique Laboratoire d’Ecologie Alpine Grenoble – “Introduction to DNA metabarcoding” (Keynote)
  • Kristy Deiner, Eawag: Swiss Federal Institute of Aquatic Science and Technology – “Biomonitoring macroinvertebrates with environmental DNA”
  • Serita Frey, University of New Hampshire – “Fungal Biodiversity: Sustaining the Wood-Wide Web in Temperate Forests”
  • John Colbourne, University of Birmingham UK – “Genomes as Indicators of Environmental Health”
  • Dorota Porazinska, University of Colorado Boulder – “Highly endemic diversity patterns of soil microscopic taxa”

Symposium Description:  High-throughput sequencing technologies now offer tremendous opportunities to make major inroads into our understanding of global biodiversity, macroecology, species detection/biomonitoring and multi-level trophic interactions. For microbial eukaryotic taxa, we can now conduct en mass biodiversity assessment using taxonomic gene markers at a fraction of the time and cost required for traditional (morphological) approaches. Complimented by metagenomics, metatranscriptomics, metabarcoding of larger organismal communities and the analysis of “free” environmental DNA (eDNA), the possibilities of enhancing current approaches to biodiversity are vast. In addition, as databases of genes with functional descriptions expand and links between genotype and phenotype extend, metagenomic approaches become useful for linking functional diversity and ecosystem function. Despite this promise, current bottlenecks and roadblocks lie in the development of useful distributed tools, links between molecules and morphology/ecology, and common data standards to allow global comparisons across individual studies. In order to make the most of emerging high-throughput sequencing approaches, we must draw on expertise from diverse disciplines, including microbial, molecular and contemporary ecology. The goal of this session is to catalyze cross-disciplinary discussions between the ecology and environmental sequencing communities and showcase the opportunities that currently exist for 21st Century ecologists. This session will begin with an overview of environmental sequencing approaches, introducing participants to the methods, data types and current advantages and limitations of DNA-based studies. This session would stimulate critical discussion related to the 2014 meeting theme of “Biodiversity and Ecosystem Services,” with interdisciplinary links to other international and EU-focused topics (Marine, Freshwater, and Agro-ecology). Since community-based molecular genetic analysis  represents an emerging ecological discipline, it is important to enhance linkages between the environmental DNA community and those focusing on contemporary ecological challenges, to facilitate high-throughput ecological research that will be relevant at the European scale.

This BES session proposal is timely: The understanding of patterns and mechanisms of biodiversity is among the central goals of ecology, yet patterns of the diversity of microscopic organisms continues to remain greatly uncharacterized and unexplored. Spatial patterns of species diversity are important because they generate knowledge for setting priorities for conservation, monitoring, and restoration programs that are strongly advocated in the European Union. Given that microscopic taxa are major components of detrital foodwebs and play key roles as decomposers, predators and parasites, the application of high-throughput sequencing is critical for expediting our understanding of species’ diversity and functional attributes.

 

ESA 2014 – Workshop materials posted

Thanks to everyone for coming out to our workshop at the ESA 2014 annual meeting, entitled “Environmental sequencing approaches and computational tools for ecologists”. We had a great group of participants who helped facilitate some very productive discussions!

Our workshop materials have now been posted online:

  • QIIME demonstration and discussion (PDF slides – Dorota Porazinska and Zhenjiang Xu, University of Colorado, Boulder) Topics covered:
    • Demonstration with default vs. modified parameters in software workflows (covering the different options possible, and how to modify them for different datasets and questions)
    • Explanation of how files are generated, what the software outputs look like, and how users can make use of the different files
    • Discussion will include data visualization tools for data analysis and exploration

NSF BIO seeks community input on Genomes-Phenomes Research frontiers

This e-mail announcement from the US National Science Foundation may be of interest to RCN EukHiTS network participants:

BIO seeks community input on Genomes-Phenomes research frontiers: John Wingfield, Assistant Director of the National Science Foundation Directorate for Biological Sciences (BIO), is pleased to announce the posting of a Wiki to seek community input on the grand challenge of understanding the complex relationship between genomes and phenomes.  The Wiki is intended to facilitate discussion among researchers in diverse disciplines that intersect with biology, such as computation, mathematics, engineering, physics, and chemistry.The Wiki format encourages open communication, captures new viewpoints, and promotes free exchange of ideas about the bottlenecks that impede progress on the genomes-phenomes grand challenge and approaches or strategies to overcome these challenges. Information provided through the Wiki will help inform BIO’s future research investments and activities relevant to understanding genomes-phenomes relationships.To provide comments, ask questions and view input from and interact with other community members, first-time users should sign up for an account via this link: Sign-up. Once registered, users will be directed to the main page of the NSF Wiki to accept the terms and conditions before proceeding. Additional guidance and subsequent visits can be accessed via this link: Genomes-Phenomes Wiki. Community members should feel free to forward notice of this to anyone they think might be interested in contributing to the discussion. Questions regarding the Wiki should be sent to bio-gen-phen@nsf.gov.