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Using FlyBase, a Database of Drosophila Genes and Genomes [chapter]

Steven J. Marygold, Madeline A. Crosby, Joshua L. Goodman
2016 Msphere  
For nearly 25 years, FlyBase (flybase.org) has provided a freely available online database of biological information about Drosophila species, focusing on the model organism D. melanogaster. The need for a centralized, integrated view of Drosophila research has never been greater as advances in genomic, proteomic and high-throughput technologies add to the quantity and diversity of available data and resources. FlyBase has taken several approaches to respond to these changes in the research
more » ... scape. Novel report pages have been generated for new reagent types and physical interaction data; Drosophila models of human disease are now represented and showcased in dedicated Human Disease Model Reports; other integrated reports have been established that bring together related genes, datasets or reagents; Gene Reports have been revised to improve access to new data types and to highlight functional data; links to external sites have been organized and expanded; and new tools have been developed to display and interrogate all these data, including improved batch processing and bulk file availability. In addition, several new community initiatives have served to enhance interactions between researchers and FlyBase, resulting in direct user contributions and improved feedback. This chapter provides an overview of the data content, organization and available tools within FlyBase, focusing on recent improvements. We hope it serves as a guide for our diverse user base, enabling efficient and effective exploration of the database and thereby accelerating research discoveries.
doi:10.1007/978-1-4939-6371-3_1 pmid:27730573 pmcid:PMC5107610 fatcat:gbtsjk6xj5esbp6wt6ttdswhp4

Relevant and Robust

Noah D. Goodman, Michael C. Frank, Thomas L. Griffiths, Joshua B. Tenenbaum, Peter W. Battaglia, Jessica B. Hamrick
2015 Psychological Science  
Over the past 15 years, probabilistic modeling of human cognition has yielded quantitative theories of a wide variety of phenomena (Tenenbaum, Kemp, Griffiths, & Goodman, 2011) .  ...  For instance, they showed that data on pragmatic inference (Frank & Goodman, 2012) are inconsistent with an alternative variant of the proposed model that uses a hard-max rather than a soft-max function  ...  Goodman Marcus and Davis (2013) Author Contributions All authors contributed to writing this manuscript.  ... 
doi:10.1177/0956797614559544 pmid:25749699 fatcat:s7cbbtpd5bgcjo5gwkagk65thu

FlyBase: improvements to the bibliography

Steven J. Marygold, Paul C. Leyland, Ruth L. Seal, Joshua L. Goodman, Jim Thurmond, Victor B. Strelets, Robert J. Wilson
2012 Nucleic Acids Research  
An accurate, comprehensive, non-redundant and up-to-date bibliography is a crucial component of any Model Organism Database (MOD). Principally, the bibliography provides a set of references that are specific to the field served by the MOD. Moreover, it serves as a backbone to which all curated biological data can be attributed. Here, we describe the organization and main features of the bibliography in FlyBase (flybase.org), the MOD for Drosophila melanogaster. We present an overview of the
more » ... ent content of the bibliography, the pipeline for identifying and adding new references, the presentation of data within Reference Reports and effective methods for searching and retrieving bibliographic data. We highlight recent improvements in these areas and describe the advantages of using the FlyBase bibliography over alternative literature resources. Although this article is focused on bibliographic data, many of the features and tools described are applicable to browsing and querying other datasets in FlyBase.
doi:10.1093/nar/gks1024 pmid:23125371 pmcid:PMC3531214 fatcat:hibhwutfvbashm6jsnxgadwpku

One and Done? Optimal Decisions From Very Few Samples

Edward Vul, Noah Goodman, Thomas L. Griffiths, Joshua B. Tenenbaum
2014 Cognitive Science  
, 1996; motor action: Maloney, Trommershauser, & Landy, 2007; language: Chater & Manning, 2006; decision making: McKenzie, 1994; causal judgments: Griffiths & Tenenbaum, 2005 ; and concept learning: Goodman  ...  The first problem is highlighted by an intriguing observation from Goodman et al. (2008) about performance in categorization tasks in which people see positive and negative exemplars of a category and  ... 
doi:10.1111/cogs.12101 pmid:24467492 fatcat:rbyl6vvlnjazvdq6yg26klyufy

Help or Hinder: Bayesian Models of Social Goal Inference

Tomer Ullman, Chris L. Baker, Owen Macindoe, Owain Evans, Noah D. Goodman, Joshua B. Tenenbaum
2009 Neural Information Processing Systems  
Inferences of simple relational goals between agents (such as chasing and fleeing) from maze-world interactions were considered by Baker, Goodman and Tenenbaum [1] , using multiagent MDP-based inverse  ... 
dblp:conf/nips/UllmanBMEGT09 fatcat:3qkc3pg57bb3bmjedtxbpj4fcm

Exploring FlyBase Data Using QuickSearch

Steven J. Marygold, Giulia Antonazzo, Helen Attrill, Marta Costa, Madeline A. Crosby, Gilberto dos Santos, Joshua L. Goodman, L. Sian Gramates, Beverley B. Matthews, Alix J. Rey, Jim Thurmond
2016 Current Protocols in Bioinformatics  
FlyBase (flybase.org) is the primary online database of genetic, genomic and functional information about Drosophila species, with a major focus on the model organism Drosophila melanogaster. The long and rich history of Drosophila research, combined with recent surges in genomic-scale and high-throughput technologies, mean that FlyBase now houses a huge quantity of data. Researchers need to be able to rapidly and intuitively query these data, and the QuickSearch tool has been designed to meet
more » ... hese needs. This tool is conveniently located on the FlyBase homepage and is organized into a series of simple tabbed interfaces that cover the major data and annotation classes within the database. This unit describes the functionality of all aspects of the QuickSearch tool. With this knowledge, FlyBase users will be equipped to take full advantage of all QuickSearch features and thereby gain improved access to data relevant to their research.
doi:10.1002/cpbi.19 pmid:27930807 pmcid:PMC5152691 fatcat:gak43qcvjndcphz774srcxvzkq

FlyBase: establishing a Gene Group resource forDrosophila melanogaster

Helen Attrill, Kathleen Falls, Joshua L. Goodman, Gillian H. Millburn, Giulia Antonazzo, Alix J. Rey, Steven J. Marygold
2015 Nucleic Acids Research  
Many publications describe sets of genes or gene products that share a common biology. For example, genome-wide studies and phylogenetic analyses identify genes related in sequence; high-throughput genetic and molecular screens reveal functionally related gene products; and advanced proteomic methods can determine the subunit composition of multiprotein complexes. It is useful for such gene collections to be presented as discrete lists within the appropriate Model Organism Database (MOD) so
more » ... researchers can readily access these data alongside other relevant information. To this end, FlyBase (flybase.org), the MOD for Drosophila melanogaster, has established a 'Gene Group' resource: high-quality sets of genes derived from the published literature and organized into individual report pages. To facilitate further analyses, Gene Group Reports also include convenient download and analysis options, together with links to equivalent gene groups at other databases. This new resource will enable researchers with diverse backgrounds and interests to easily view and analyse acknowledged D. melanogaster gene sets and compare them with those of other species.
doi:10.1093/nar/gkv1046 pmid:26467478 pmcid:PMC4702782 fatcat:2ljorlbf4jgkrilfxniusk6pcy

FlyBase: A guided tour of highlighted features

L Sian Gramates, Julie Agapite, Helen Attrill, Brian R Calvi, Madeline A Crosby, Gilberto dos Santos, Joshua L Goodman, Damien Goutte-Gattat, Victoria K Jenkins, Thomas Kaufman, Aoife Larkin, Beverley B Matthews (+2 others)
2022 Genetics  
At the time of writing, members of the FlyBase Consortium included: Norbert Perrimon, Susan Russo Gelbart, Julie Agapite, Kris Broll, Lynn Crosby, Gil dos Santos, Kathleen Falls, L.  ...  Attrill, Phani Garapati, Damien Goutte-Gattat, Aoife Larkin, Steven Marygold, Alex McLachlan, Gillian Millburn, Arzu O ¨ztu ¨rk-C¸olak, Clare Pilgrim, Vitor Trovisco, Brian Calvi, Thomas Kaufman, Josh Goodman  ... 
doi:10.1093/genetics/iyac035 pmid:35266522 pmcid:PMC8982030 fatcat:bvoxngtcxzcrhhl7prxhf7uxxy

The imaginary fundamentalists: The unshocking truth about Bayesian cognitive science

Nick Chater, Noah Goodman, Thomas L. Griffiths, Charles Kemp, Mike Oaksford, Joshua B. Tenenbaum
2011 Behavioral and Brain Sciences  
., Goodman et al. 2008b ). This is entirely in line with practice in other modeling frameworks. (ii) J&L are concerned that Bayesians downplay the structure of the environment.  ...  ., Anderson 1991b; Goodman et al. 2008b; Steyvers et al. 2009; .  ... 
doi:10.1017/s0140525x11000239 fatcat:spa6vwghifdfjonvjffbebdv5i

Microparticles impact coagulation after traumatic brain injury

Emily F. Midura, Peter L. Jernigan, Joshua W. Kuethe, Lou Ann Friend, Rosalie Veile, Amy T. Makley, Charles C. Caldwell, Michael D. Goodman
2015 Journal of Surgical Research  
For EXTEM and FIBTEM analysis, 20 μL of thromboplastin and cytochalasin D were added to 300 μL of citrated blood.  ...  Treated samples had 30 μL of saline or MP preparations added. MPs were isolated as described in section 2.5.  ... 
doi:10.1016/j.jss.2015.02.064 pmid:25846728 pmcid:PMC5857955 fatcat:2vazg2kkgffnfmuzm53bpqov2q

Identification of Differential Item Functioning in Assessment Booklet Designs With Structurally Missing Data

Joshua T. Goodman, John T. Willse, Nancy L. Allen, John S. Klaric
2011 Educational and Psychological Measurement  
Goodman, John T. Willse?, Nancy L. Allen’, and John S.  ...  Goodman et al. ge 93 Allen, N. L., Donoghue, J. R., & Schoeps, T. L. (2001). The NAEP 1998 technical report (NCES Publication No. 2001-509). Washington, DC: National Center for Education Statistics.  ... 
doi:10.1177/0013164410387341 fatcat:ejx2twakwjdpzhdwk2qu7j3o2a

Acute Effects of Cocaine on Human Brain Activity and Emotion

Hans C Breiter, Randy L Gollub, Robert M Weisskoff, David N Kennedy, Nikos Makris, Joshua D Berke, Julie M Goodman, Howard L Kantor, David R Gastfriend, Jonn P Riorden, R.Thomas Mathew, Bruce R Rosen (+1 others)
1997 Neuron  
NAc/SCC R 6 7 Ϫ9 7ϫ10 Ϫ6 1.5 9/10 φ ϩ L Ϫ6 1 3 0 4ϫ10 Ϫ6 1.5 8/10 φ ϩ Caudate R 13 Ϫ3 2 2 5ϫ10 Ϫ7 0.8 8/10 ϩ Ϫ L Ϫ 9 Ϫ 3 1 9 3ϫ10 Ϫ7 1.0 7/10 ϩ φ Putamen R 28 7 Ϫ3 4ϫ10 Ϫ8 1.4 8/10 ϩ Ϫ L Ϫ 28 7 Ϫ3 N S(  ...  5ϫ10 Ϫ5 ) 0.5 5/10 φ φ BF/GP R 22* 1* Ϫ6* NS φ 6/10 φ ϩ L Ϫ19 0 Ϫ3 6ϫ10 Ϫ9 1.8 7/10 ϩ Ϫ Thalamus aThal R 3 Ϫ18 13 6 ϫ 10 Ϫ8 0.4 8/10 φ φ L φ φ φ NS φ 7/10 φ φ pThal R 6 Ϫ25 16 9 ϫ 10 Ϫ7 1.4 8/10 ϩ φ L  ... 
doi:10.1016/s0896-6273(00)80374-8 pmid:9331351 fatcat:2o3vumytbzfzdcfdv4d3at2gza

Advancing methods for US transgender health research

Sari L. Reisner, Madeline B. Deutsch, Shalender Bhasin, Walter Bockting, George R. Brown, Jamie Feldman, Rob Garofalo, Baudewijntje Kreukels, Asa Radix, Joshua D. Safer, Vin Tangpricha, Guy T'Sjoen (+1 others)
2016 Current Opinion in Endocrinology, Diabetes & Obesity  
Purpose of Review-To describe methodological challenges, gaps, and opportunities in U.S. transgender health research. Recent Findings-Lack of large prospective observational studies and intervention trials, limited data on risks and benefits of gender affirmation (e.g., hormones and surgical interventions), and inconsistent use of definitions across studies hinder evidence-based care for transgender people. Systematic high-quality observational and intervention-testing studies may be carried
more » ... using several approaches, including general population-based, health systems-based, clinic-based, venue-based, and hybrid designs. Each of these approaches has its strength and limitations; however, harmonization of research efforts is needed. Ongoing development of evidence-based clinical recommendations will benefit from a series of observational and intervention studies aimed at identification, recruitment, and follow-up of transgender people of different ages, from different racial, ethnic, and socioeconomic backgrounds and with diverse gender identities. Summary-Transgender health research faces challenges that include standardization of lexicon, agreed-upon population definitions, study design, sampling, measurement, outcome ascertainment, and sample size. Application of existing and new methods is needed to fill existing gaps, increase the scientific rigor and reach of transgender health research, and inform evidencebased prevention and care for this underserved population. Keywords transgender; research methods; health disparity Reisner et al.
doi:10.1097/med.0000000000000229 pmid:26845331 pmcid:PMC4916925 fatcat:iwasageobnfpvlkzfgrgoyi4iy

FlyBase at 25: looking to the future

L. Sian Gramates, Steven J. Marygold, Gilberto dos Santos, Jose-Maria Urbano, Giulia Antonazzo, Beverley B. Matthews, Alix J. Rey, Christopher J. Tabone, Madeline A. Crosby, David B. Emmert, Kathleen Falls, Joshua L. Goodman (+6 others)
2016 Nucleic Acids Research  
Since 1992, FlyBase (flybase.org) has been an essential online resource for the Drosophila research community. Concentrating on the most extensively studied species, Drosophila melanogaster, FlyBase includes information on genes (molecular and genetic), transgenic constructs, phenotypes, genetic and physical interactions, and reagents such as stocks and cDNAs. Access to data is provided through a number of tools, reports, and bulk-data downloads. Looking to the future, FlyBase is expanding its
more » ... ocus to serve a broader scientific community. In this update, we describe new features, datasets, reagent collections, and data presentations that address this goal, including enhanced orthology data, Human Disease Model Reports, protein domain search and visualization, concise gene summaries, a portal for external resources, video tutorials and the FlyBase Community Advisory Group.
doi:10.1093/nar/gkw1016 pmid:27799470 pmcid:PMC5210523 fatcat:nw3to6susnfplnfpo54pxqw27a

Percutaneous Gastrostomy of the Excluded Gastric Segment after Roux-en-Y Gastric Bypass Surgery

Evan G. Stein, Jacob Cynamon, Marc Joshua Katzman, Elliott Goodman, Alla Rozenblit, Ellen L. Wolf, Marcy B. Jagust
2007 Journal of Vascular and Interventional Radiology  
A new technique for percutaneous gastrostomy of a decompressed excluded gastric segment after Roux-en-Y gastric bypass (RYGBP) surgery is described and the results in a single institution are reviewed. Computed tomography guidance was used to place a 21-or 22-gauge needle into the lumen of the stomach and distend it to allow placement of a feeding catheter. Ten women underwent the procedure, and despite only three patients having clear access windows, gastrostomy placement was ultimately
more » ... ful in all 10 patients. Percutaneous gastrostomy of the decompressed excluded gastric segment after RYGBP surgery can be challenging, but a high rate of success can be achieved. J Vasc Interv Radiol 2007; 18:914 -919 Abbreviation: RYGBP ϭ Roux-en-Y gastric bypass From the
doi:10.1016/j.jvir.2007.03.001 pmid:17609454 fatcat:bjacl4u7obddnfr4lunzi7fabe
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