Robert Robbins

Background: Efforts to harmonize genomic data standards used by the biodiversity and metagenomic research communities have shown that prokaryotic data cannot be understood or represented in a traditional, classical biological context for conceptual reasons, not technical ones.

This conference was held in St. Petersburg Beach, Florida June 4--7, 1992. The purpose of this conference was to provide a forum for exchange of state-of-the-art information in the field of the human genome. This provided an opportunity to gain firsthand knowledge of the scope, direction, and future prospects of information and computing in complex genome analysis. Topics of discussion

Progress on the project to study the effects of the ELF Communication System on small mammals and nesting birds is detailed for the base period, 1982. Initial population surveys were conducted which showed that the main study species, the Black-capped Chickadee (Parus atricapillus) and the deer-mouse, (Peromyscus gracilis) were present and abundant on the pilot plot and several other plots which are potential sites for establishing permanent plots once the route of the ELF antenna is known. The pilot plot will serve as a testing site for studies of parental care, nestling growth and maturation, fecundity, homing, activity patterns, embryological development and metabolic physiology. Nesting boxes were placed on the pilot plot in September and October, 1982, to insure that animals would be available for these studies in the spring, 1983. A data-base management system was developed to coordinate the collection and analysis of data for the planned studies.

This position paper, Data Management for LTER: 1980 – 2010, was independently prepared by Dr. Robert J. Robbins, a member of the 30 Year LTER Review Committee. This position paper is not part of the LTER 30 Year Review Report but is provided by the BIO Advisory Committee without comment or endorsement as an independent perspective regarding LTER data management. Jose' N. Onuchic, Chair, BIO Advisory Committee BIO 12-002

A traditional drawing of the tree of life emphasizes the eukaryota. Classical biology has largely been the study of somatic tissue in multi-cellular eukaryotes. Yet the eukaryotes represent a highly specialized and highly constrained form of life. Attempts to understand biological dark matter -- the invisible prokaryotic realm -- by generalizing from studies on eukaryota cannot succeed. As metagenomic tools allow the study of the prokaryotic realm, we are discovering this truly is a microbial planet. The macroscopic organisms -- the subject of classical biology -- are just lumps in the microbial soup.

GBWG (the GSC Biodiversity Working Group, with assistance from RCN4GSC) is reaching out to other communities to engage scientists at the interface of genomics and biodiversity. The NSF RCN4GSC project at UCSD has the mission to: create a research coordination network to promote and integrate standards for genomic and metagenomic data and metadata within an international community. The network is based on the existing Genomic Standard Consortium and will be extended under this award to include ecological data standards such as Ecological Metadata Language, biodiversity standards such as Darwin Core, and environmental research programs such as the Global Lake Ecological Observatory Network and Long Term Ecological Research. Why the big push into biodiversity? • Biodiversity is less a field of biology than a perspective (that of variance) into biology. • Diversity is a sine qua non of biology; no diversity, no evolution. • Genetics / genomics are equally central to biology. • Probably ...

The most fundamental unit of traditional biodiversity - the individual organism (defined as a physically connected, multi-cellular aggregation, with all of the cells clonally derived from one ancestral cell) - has no parallel in the world of prokaryotic biology. Yet recent advances (metagenomics tools, etc) have shown that about half of the world's biomass and by far most of its physiological (as opposed to morphological, or mechanical) biodiversity occurs in the prokaryotic realm. Other work is establishing that symbiosis (in the sense of the bio-outsourcing of some key biological functions) is far more common than traditionally recognized. In fact, because horizontal gene transfer (HGT) occurs without regard for species boundaries, it is now becoming clear that some microbial genes are more attributes of a particular ecosystem than of a particular individual or species. (This is why, for example, the same "cassette" of pathology genes is often found spreading across ...

Public Release: 12/09/2011 Dear Colleagues: The Advisory Committee for the Biological Sciences (BIO AC) has approved the Long Term Ecological Research Program Report of the 30 Year Review Committee for public posting on the Advisory Committee web site. The BIO AC retains its prerogative to comment on the content of the report at a future date. The Advisory Committee would like to thank the Review Committee for its efforts in preparing this important report. Sincerely, Barbara Schaal, Ph.D. , ChairL Advisory Committee for the Biological Sciences This report was prepared by the participants of the review committee. Any opinions, findings, conclusions, or recommendations expressed in this report are those of the participants and do not necessarily represent the official views, opinions, or policy of the National Science Foundation. BIO 12-001

ABSTRACT Informatics of some kind will play a role in every aspect of the Human Genome Project (HGP): data acquisition, data analysis, data exchange, data publication and, data visualization. What are the real requirements and challenges? The primary requirement is clear thinking and the main challenge is design. If good design is lacking, the price will be failure of genome informatics and ultimately failure of the genome project itself. We need good designs to deliver the tools necessary for acquiring and analyzing DNA sequences. As these tools become more efficient, we will need new tools for comparative genomic analyses. To make the tools work, we will need to address and solve nomenclature issues that are essential, if also tedious. We must devise systems that will scale gracefully with the increasing flow of data. We must be able to move data easily from one system to another, with no loss of content. As scientists, we will have failed in our responsibility to share results, should repeating experiments ever become preferable to searching the literature. Our databases must become a new kind of scientific literature and we must develop ways to make electronic data publishing as routine as traditional journal publishing. Ultimately, we must build systems so advanced that they are virtually invisible. In summary, the HGP can be considered the most ambitious, most audacious information-management project ever undertaken. In the HGP, computers will not merely serve as tools for cataloging existing knowledge. Rather, they will serve as instruments, helping to create new knowledge by changing the way we see the biological world. Computers will allow us to see genomes, just as radio telescopes let us see quasars and electron microscopes let us see viruses.

Version 5.0 of the Genome Data Base (GDB) was released in March 1993. This document describes some of the significant changes to the types of data which are stored within the GDB. In addition to handling a wider scope of data, the GDB 5.0 application software now supports the X-Windows protocol. Although the GDB software still remains the most widely utilized method for accessing the data, alternate methods of access are now available, including direct SQL (Structured Query Language) queries, FTP (Internet File Transfer Protocol), WAIS (Wide Area Information Server), and other tools produced by third-party developers.

The variable white mutation arose spontaneously in 1983 within a laboratory stock of wild-type deer mice (Peromyscus maniculatus). The original mutant animal was born to a wild-type pair that had previously produced several entirely wild-type litters. Other variable white animals were bred from the initial individual. Variable white deer mice exhibit extensive areas of white on the head, sides, and tail. Usually a portion of pigmented pelage occurs dorsally and on the shoulders, but the extent of white varies from nearly all white to patches of white on the muzzle, tip of tail, and sides. The pattern is irregular, but not entirely asymmetrical. Eyes are pigmented, but histologically reveal a decrease in thickness and pigmentation of the choroid layer. Many variable white animals do not respond to auditory stimuli, an effect that is particularly evident in animals in which the head is entirely white. Ataxic behavior is also prevalent. Pigment distribution, together with auditory and ...

An autosomal recessive mutation affecting hair and eye pigmentation was discovered in the F2 progeny of wild-type deer mice, (Peromyscus maniculatus), trapped near East Lansing, Michigan. When homozygous, the mutation (designated as blonde, bl), reduces both black and yellow pigmentation deposited in the fur, reduces or eliminates pigmentation in the non-follicular melanocytes of the outer ear, peri-orbital skin and tail, slightly reduces the amount of pigmentation in the choroidal melanocytes, and completely eliminates pigmentation of the retinal epithelium.

Much is written about Internet access, Web access, Web site accessibility, and access to online health information. The term access has, however, a variety of meanings to authors in different contexts when applied to the Internet, the Web, and interactive health communication. We have summarized those varied uses and definitions and consolidated them into a framework that defines Internet and Web access issues for health researchers. We group issues into two categories: connectivity and human interface. Our focus is to conceptualize access as a multicomponent issue that can either reduce or enhance the public health utility of electronic communications.

Microbial ecology has been enhanced greatly by the ongoing 'omics revolution, bringing half the world's biomass and most of its biodiversity into analytical view for the first time; indeed, it feels almost like the invention of the microscope and the discovery of the new world at the same time. With major microbial ecology research efforts accumulating prodigious quantities of sequence, protein, and metabolite data, we are now poised to address environmental microbial research at macro scales, and to begin to characterize and understand the dimensions of microbial biodiversity on the planet. What is currently impeding progress is the need for a framework within which the research community can develop, exchange and discuss predictive ecosystem models that describe the biodiversity and functional interactions. Such a framework must encompass data and metadata transparency and interoperation; data and results validation, curation, and search; application programming interfaces for modeling and analysis tools; and human and technical processes and services necessary to ensure broad adoption. Here we discuss the need for focused community interaction to augment and deepen established community efforts, beginning with the Genomic Standards Consortium (GSC), to create a science-driven strategic plan for a Genomic Software Institute (GSI).

This report details the outcome of the 13(th) Meeting of the Genomic Standards Consortium. The three-day conference was held at the Kingkey Palace Hotel, Shenzhen, China, on March 5-7, 2012, and was hosted by the Beijing Genomics Institute. The meeting, titled From Genomes to Interactions to Communities to Models, highlighted the role of data standards associated with genomic, metagenomic, and amplicon sequence data and the contextual information associated with the sample. To this end the meeting focused on genomic projects for animals, plants, fungi, and viruses; metagenomic studies in host-microbe interactions; and the dynamics of microbial communities. In addition, the meeting hosted a Genomic Observatories Network session, a Genomic Standards Consortium biodiversity working group session, and a Microbiology of the Built Environment session sponsored by the Alfred P. Sloan Foundation.