Monthly Archives: March 2010

Using windows ‘safely’

This topic has come up a few times in the lab recently, so I decided to write a guide on it. I’ll omit the Linux advertisement, but if you are going to (or have to) use windows for something, here are some good practices. All of these tools are (at the time of this writing) free to the public for home use.

Back up important stuff. This goes for everyone, actually. (Never mind the bit about me not practicing what I preach…)

Use avast! antivirus. It is fairly unobtrusive and has its virus definitions updated really often. If you don’t like avast!, people alternatively use AVG (although they’re getting better and better at hiding the free version). I believe that both programs come set up automatically, but you should make sure that your software is A. updating itself regularly and B. actually performing scans at some point.

Anti-spyware stuff tends to be good too. Antivirus will catch some of this, and they’re better and better at it lately, but I still prefer to use a cocktail of anti-bad-stuff on my windows machines. I recommend using a combination of Spybot Search & Destroy and Ad-Aware. NOTE: it seems that, unfortunately, Ad-Aware has gone the way of ZoneAlarm. The link to the free version exists but is broken. Gross. If you can find a free version of it please post the link. Otherwise, I must unfortunately recommend that readers do not install Ad-Aware by jumping through the hoop of their stupid “complete one offer” scam. Be sure to update your anti-spyware after you install it. Spybot in particular has an “Immunize” function in addition to scanning. This is perhaps the biggest motivator for installing spybot. Blocking spyware entirely is awesome, and makes sure you waste less time removing stuff over and over.

Use Firefox. (Chrome seems cool too, but I don’t have any tips for securing Chrome, or much knowledge about it in general). Lock down your Firefox using NoScript and AdBlock Plus. NOTE: After installing these two plugins, websites are going to look a little…different. Particularly NoScript. There will be a little ‘S’ in the bottom right hand corner of your Firefox now that you will often have to click and tell it to ‘allow’ scripts from certain trusted websites. This can be annoying at first, but is worth the added security, especially if you tell it to remember your choice and always trust Google.com, slashdot.org, sourceforge.net, Edwardslab.sdsu.edu or whatever. Basically, any site you know isn’t trying to do something to your computer you can trust, but beware that the plugin is only as good as your decisions are.

I also recommend WebOfTrust for finding out what websites are shady or not in the first place.

I hope these links help you secure your Windows install. If you have any questions about using the aforementioned software, feel free to ask in the comments or email me and I’ll do my best to help!

PhiGenometrics1

Phage Genometrics. I’m only 23 years late!

“Eureka! If I just ran these analyses 23 years earlier!”

This is what I was telling myself few minutes after I was so excited at looking at the nice graphs I generated by analyzing the GC% statistics of about 600 phage genomes (graphs below).

As any good scientist (although they would tell you otherwise), I did the analysis before digging the literature deeply. I just got this urge to perform all kind of calculations on the phage codons and compare them to the phage overall GC%. Of course I know well that the third nucleotide in a codon is under much less pressure than other nucleotides, and thus varies depending on which genome it is located in (depending on many factors including the translational machinery of the host). However, I didn’t know whether anybody bothered to look at the difference between codon GC statistics and genome GC statistics, or the slopes of codon GC% versus genome GC%.

Whether the data below are new or not (they are new of course, since they are done on new sequences, but old since the conclusion was reached in 1987–before some of our lab members were born–, or maybe earlier), the figures look really cool! Another neat study from 1997 is here.

PhiGenometrics1

Fig. 1: GC% statistics for individual protein-coding genes (all phage proteins in PhAnToMe)

PhiGenometrics2

Fig. 2: GC% statistics for individual phages (all phages in PhAnToMe)

PhiGenometrics3

Fig. 3: nucleotide GC% (first and second derivatives) vs genome GC% statistics for individual phages (all phages in PhAnToMe)

publist

2012

 

  1. Hanna LF, Matthews TD, Dinsdale EA, Hasty D, Edwards RA. Characterization of the ELPhiS Prophage from Salmonella enterica serovar Enteritidis strain LK5. Appl Environ Microbiol. 2012. [PMID: 22247173]

  2. McNair K, Bailey BA, Edwards RA. PHACTS, a computational approach to classifying the lifestyle of phages. Bioinformatics 2012. [PMID: 22238260]

  3. Schmieder R and Edwards R. Insights into antibiotic resistance through metagenomic approaches. Future Microbiol. 2012. [PMID: 22191448]

  4. Schmieder R, Lim YW, Edwards R. Identification and removal of ribosomal RNA sequences from metatranscriptomes. Bioinformatics 2012. [PMID: 22155869]

  5. Berg Miller ME, Yeoman CJ, Chia N, Tringe SG, Angly FE, Edwards RA, Flint HJ, Lamed R, Bayer EA, White BA. Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome. Environ Microbiol. 2012 [PMID: 22004549]

  6. Espinoza-Valles I, Soto-Rodríguez S, Edwards RA, Wang Z, Vora GJ, Gómez-Gil B. Draft Genome Sequence of the Shrimp Pathogen Vibrio harveyi CAIM 1792. J Bacteriol. 2012 [PMID: 22461546]

  7. Dwivedi B, Schmieder R, Goldsmith DB, Edwards RA, Breitbart M. PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity. BMC Bioinformatics. 2012 [PMID: 22385976]

  8. Li JW, Schmieder R, Ward RM, Delenick J, Olivares EC, Mittelman D. SEQanswers: An open access community for collaboratively decoding genomes. Bioinformatics. 2012 [PMID: 22419780]

  9. Luckwu de Lucena BT, Silva GG, Manoel Dos Santos B, Dias GM, Amaral GR, Moreira AP, de Morais Júnior MA, Dutilh BE, Edwards RA, Balbino V, Thompson CC, Thompson FL. Genome sequence of the ethanol tolerant Lactobacillus vini strains LMG23202T and JP7.8.9. Journal of Bacteriology . 2012 [PMID: 22582376]

  10. Akhter S, Aziz RK, Edwards RA. PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. Nucleic Acids Research 2012 [PMID: 22584627]

  11. Garza DR, Thompson CC, Loureiro EC B, Dutilh BE, Inada DT, Junior ECS, Cardoso JF, Nunes MRT, de Lima CPS, Vellasco RS, Nunes KNB, Santos ECO, Edwards RA, Vicente ACP, Morais LLCS. Genome-Wide Study of the Defective Sucrose Fermenter Strain of Vibrio cholerae from the Latin American Cholera Epidemic. PLoS ONE 2012 [PMID: 22662140]

  12. Amaral GRS, Silva BSO, Santos EO, Dias GM, Lopes RM, Edwards RA, Thompson CC, Thompson FL. Genome Sequence of the Bacterioplanktonic, Mixotrophic Vibrio campbellii Strain PEL22A, Isolated in the Abrolhos Bank. Journal of Bacteriology 2012. [PMID: 22535939]

  13. Trindade-Silva AE, Rua C, Silva GG, Dutilh BE, Moreira AP, Edwards RA, Hajdu E, Lobo-Hajdu G, Vasconcelos AT, Berlinck RG, Thompson FL. Taxonomic and Functional Microbial Signatures of the Endemic Marine Sponge Arenosclera brasiliensis. PLoS ONE 2012. [PMID: 22768320]

  14. Hedin M, Starrett J, Akhter S, Schönhofer AL, Shultz JW. Phylogenomic Resolution of Paleozoic Divergences in Harvestmen (Arachnida, Opiliones) via Analysis of Next-Generation Transcriptome Data.PLoS ONE 2012. [PMID: 22936998]

  15. Liu JZ, Jellbauer S, Poe AJ, Ton V, Pesciaroli M, Kehl-Fie TE, Restrepo NA, Hosking MP, Edwards RA, Battistoni A, Pasquali P, Lane TE, Chazin WJ, Vogl T, Roth J, Skaar EP, Raffatellu M. Zinc Sequestration by the Neutrophil Protein Calprotectin Enhances Salmonella Growth in the Inflamed Gut. Cell Host & Microbe 2012. [PMID: 22423963]

  16. YW Lim, R Schmieder, M Haynes, D Willner, M Furlan, M Youle, K Abbott, R Edwards, et al. Metagenomics and metatranscriptomics: Windows on CF-associated viral and microbial communities. Journal of Cystic Fibrosis 2012 [Link]

  17. M Yue, R Schmieder, RA Edwards, SC Rankin, DM Schifferli. Microfluidic PCR combined with pyrosequencing identify allelic variants with phenotypic associations in targeted Salmonella genes. Applied and Environmental Microbiology 2012 [PMID: 22885744]

  18. Lynch EA, Langille MG, Darling A, Wilbanks EG, Haltiner C, Shao KS, Starr MO, Teiling C, Harkins TT, Edwards RA, Eisen JA, Facciotti MT. Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux. PLoS ONE 2012. [PMID: 22848480]

  19. M Yue, SC Rankin, RT Blanchet, JD Nulton, RA Edwards, DM Schifferli. Diversification of the Salmonella Fimbriae: A Model of Macro-and Microevolution. PLoS ONE 2012. [PMID: 22701679, PubMed – in process]

  20. Bruce T, Meirelles PM, Garcia G, Paranhos R, Rezende CE, de Moura RL, Filho RF, Coni EO, Vasconcelos AT, Amado Filho G, Hatay M, Schmieder R, Edwards R, Dinsdale E, Thompson FL. Abrolhos Bank Reef Health Evaluated by Means of Water Quality, Microbial Diversity, Benthic Cover, and Fish Biomass Data. PLoS ONE 2012. [PMID:  22679480, PubMed – in process]

  21. Noriko Cassman, Alejandra Prieto-Davó, Kevin Walsh, Genivaldo G. Z. Silva, Florent Angly, Sajia Akhter, Katie Barott, Julia Busch, Tracey McDole, J. Matthew Haggerty, Dana Willner, Gadiel Alarcón, Osvaldo Ulloa, Edward F. DeLong, Bas Dulith, Forest Rohwer, Elizabeth A. Dinsdale. Oxygen minimum zones harbor novel viral communities with low diversity. Environmental Microbiology 2012. [Accepted]

2011

  1. Cristiane C. Thompson, Michel Abanto Marin, Graciela Maria Dias, Bas E. Dutilh, Rob Edwards, Tetsuya Iida, Fabiano L. Thompson. Genome sequence of the human pathogen Vibrio cholerae Amazonia. Journal of Bacteriology 2011. [PMID: 21952545]

  2. Schmieder, R and Edwards, R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 2011. [PMID: 21278185]

  3. Julian R. Marchesi, Bas E. Dutilh, Neil Hall, Wilbert H. M. Peters, Rian Roelofs, Annemarie Boleij, Harold Tjalsma. Towards the Human Colorectal Cancer Microbiome. PLoS ONE 2011. [PMID: 21647227]

  4. Schmieder R, Edwards R. Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS One. 2011. [PMID: 21408061]

  5. Matthews TD, Rabsch W, Maloy S. Chromosomal rearrangements in Salmonella enterica serovar Typhi strains isolated from asymptomatic human carriers. MBio. 2011. [PMID: 21652779]

  6. Berg Miller ME, Yeoman CJ, Chia N, Tringe SG, Angly FE, Edwards RA, Flint HJ, Lamed R, Bayer EA, White BA. Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome. Environ Microbiol. 2011 [PMID: 22004549]

  7. Willner D, Haynes MR, Furlan M, Hanson N, Kirby B, Lim YW, Rainey PB, Schmieder R, Youle M, Conrad D, Rohwer F. Case studies of the spatial heterogeneity of DNA viruses in the cystic fibrosis lung. Am J Respir Cell Mol Biol. 2011. [PMID: 21980056]

  8. Willner D, Haynes MR, Furlan M, Schmieder R, Lim YW, Rainey PB, Rohwer F, Conrad D. Spatial distribution of microbial communities in the cystic fibrosis lung. ISME J. 2011. [PMID: 21796216]

  9. Ng TF, Willner DL, Lim YW, Schmieder R, Chau B, Nilsson C, Anthony S, Ruan Y, Rohwer F, Breitbart M. Broad surveys of DNA viral diversity obtained through viral metagenomics of mosquitoes. PLoS One. 2011. [PMID: 21674005]

  10. Maartje A.H.J. van Kessel, Bas E. Dutilh, Kornelia Neveling, Michael P. Kwint, Joris A. Veltman, Gert Flik, Mike S.M. Jetten, Peter H.M. Klaren and Huub J.M. Op den Camp Pyrosequencing of 16S rRNA gene amplicons to study the microbiota in the gastrointestinal tract of carp (Cyprinus carpio L.). AMB Express 1: 41 2011. [ISSN 2191-0855]

  11. Ramy K Aziz , Bhakti Dwivedi, Mya Breitbart, Robert A Edwards Phage Eco-Locator: a web tool for visualization and analysis of phage genomes in metagenomic data sets. BMC Bioinformatics 12(Suppl 7):A9 2011. [Link]


2010

  1. Mobberley J, Authement RN, Segall AM, Edwards RA, Slepecky RA, Paul JH: Lysogeny and sporulation in Bacillus isolates from the Gulf of Mexico. Appl. Environ. Microbiol 2010, 76:829-842. [PMID: 20008174]

  2. Aziz RK, Breitbart M, Edwards RA: Transposases are the most abundant, most ubiquitous genes in nature. Nucl. Acids Res. 2010:gkq140. [PMID: 20215432]

  3. Rodriguez-Brito B, Li L, Wegley L, Furlan M, Angly F, Breitbart M, Buchanan J, Desnues C, Dinsdale E, Edwards R, Felts B, Haynes M, Liu H, Lipson D, Mahaffy J, Martin-Cuadrado AB, Mira A, Nulton J, Pašić L, Rayhawk S, Rodriguez-Mueller J, Rodriguez-Valera F, Salamon P, Srinagesh S, Thingstad TF, Tran T, Thurber RV, Willner D, Youle M, Rohwer F: Viral and microbial community dynamics in four aquatic environments. ISME J 2010. [PMID: 20147985]

  4. Willner D, Furlan M, Schmieder R, Grasis JA, Pride DT, Relman DA, Angly FE, McDole T, Mariella RP, Rohwer F, Haynes M: Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity. Proc Natl Acad Sci U S A 2010. [PMID: 20547834]

  5. Disz T, Akhter S, Cuevas D, Olson R, Overbeek R, Vonstein V, Stevens R, Edwards RA: Accessing the SEED genome databases via Web services API: tools for programmers. BMC Bioinformatics 2010, 11:319.[PMID: 20546611]

  6. Schmieder R, Lim YW, Rohwer F, Edwards R: TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets. BMC Bioinformatics 2010, 11:341. [PMID: 20573248]

  7. F.L. Thompson, Rodrigues, T.B., Gonzalez, A., Cardoso, A. Clementino, M., Costagliola, M., Hozbor, C., Otero, E., Paranhos, R., Piccini, C., Peressutti, S., Schmieder, R., Edwards, R., Smith, M., Takiyama, L.R., Vieira, R., Artigas, L.F. 2010. Coastal bacterioplankton community diversity along a latitudinal gradient in Latin America by means of V6-tag pyrosequencing. 2010. Arch. Microbiol. [PMID: 21076816]

  8. Matthews TD, Edwards R, Maloy S. Chromosomal rearrangements formed by rrn recombination do not improve replichore balance in host-specific Salmonella enterica serovars. PLoS One. 2010. [PMID: 20976060]

 

2009

 

  1. Vega Thurber R, Willner-Hall D, Rodriguez-Mueller B, Desnues C, Edwards RA, Angly F, Dinsdale E, Kelly L, Rohwer F: Metagenomic analysis of stressed coral holobionts. Environ. Microbiol 2009, 11:2148-2163.[PMID: 19397678]

  2. Angly FE, Willner D, Prieto-Davó A, Edwards RA, Schmieder R, Vega-Thurber R, Antonopoulos DA, Barott K, Cottrell MT, Desnues C, Dinsdale EA, Furlan M, Haynes M, Henn MR, Hu Y, Kirchman DL, McDole T, McPherson JD, Meyer F, Miller RM, Mundt E, Naviaux RK, Rodriguez-Mueller B, Stevens R, Wegley L, Zhang L, Zhu B, Rohwer F: The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. PLoS Comput. Biol 2009, 5:e1000593. [PMID: 20011103]

  3. McNeil LK, Aziz RK: In silico Reconstruction of the Metabolic and Pathogenic Potential of Bacterial Genomes Using Subsystems. Genome Dyn 2009, 6:21-34. [PMID: 19696491]

  4. Willner D, Furlan M, Haynes M, Schmieder R, Angly FE, Silva J, Tammadoni S, Nosrat B, Conrad D, Rohwer F: Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals. PLoS ONE 2009, 4:e7370. [PMID: 19816605]

  5. Breitbart M, Hoare A, Nitti A, Siefert J, Haynes M, Dinsdale E, Edwards R, Souza V, Rohwer F, Hollander D: Metagenomic and stable isotopic analyses of modern freshwater microbialites in Cuatro Ciénegas, Mexico. Environ. Microbiol 2009, 11:16-34. [PMID: 18764874]

  6. Wagner, C., Salamon, A., Edwards, R.A., Rohwer, F., and P. Salamon. 2009. Deviations from Ultrametricity in Phage Protein Distances. Open Systems & Information Dynamics 16:75–84 [DOI: 10.1142/S1230161209000062]

  7. Brulc, J.M., Antonopoulos, D.A., Berg Miller, M.E., Wilson, M.K., Yannarell, A.C., Dinsdale, E.A., Edwards, R.A. Frank, E.D., Emerson, J.B., Wacklin, P., Coutinho, P.M., Henrissat, B., Nelson, K.E., and White, B.A.. 2009 Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proc Natl Acad Sci USA. 106:1948 –1953 [PMID: 19181843]

 

2008

 

  1. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O: The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008, 9:75. [PMID: 18261238]

  2. Dinsdale EA, Pantos O, Smriga S, Edwards RA, Angly F, Wegley L, Hatay M, Hall D, Brown E, Haynes M, Krause L, Sala E, Sandin SA, Thurber RV, Willis BL, Azam F, Knowlton N, Rohwer F: Microbial ecology of four coral atolls in the Northern Line Islands. PLoS ONE 2008, 3:e1584. [PMID: 18301735]

  3. Qu A, Brulc JM, Wilson MK, Law BF, Theoret JR, Joens LA, Konkel ME, Angly F, Dinsdale EA, Edwards RA, Nelson KE, White BA: Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome. PLoS ONE 2008, 3:e2945. [PMID: 18698407]

  4. Mou X, Sun S, Edwards RA, Hodson RE, Moran MA: Bacterial carbon processing by generalist species in the coastal ocean. Nature 2008, 451:708-711. [PMID: 18223640]

  5. Desnues C, Rodriguez-Brito B, Rayhawk S, Kelley S, Tran T, Haynes M, Liu H, Furlan M, Wegley L, Chau B, Ruan Y, Hall D, Angly FE, Edwards RA, Li L, Thurber RV, Reid RP, Siefert J, Souza V, Valentine DL, Swan BK, Breitbart M, Rohwer F: Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature 2008, 452:340-343. [PMID: 18311127]

  6. Krause L, Diaz NN, Goesmann A, Kelley S, Nattkemper TW, Rohwer F, Edwards RA, Stoye J: Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Res 2008, 36:2230-2239. [PMID: 18285365]

  7. Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, Brulc JM, Furlan M, Desnues C, Haynes M, Li L, McDaniel L, Moran MA, Nelson KE, Nilsson C, Olson R, Paul J, Brito BR, Ruan Y, Swan BK, Stevens R, Valentine DL, Thurber RV, Wegley L, White BA, Rohwer F: Functional metagenomic profiling of nine biomes. Nature 2008, 452:629-632. [PMID: 18337718]

  8. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, Ashburner M, Axelrod N, Baldauf S, Ballard S, Boore J, Cochrane G, Cole J, Dawyndt P, De Vos P, DePamphilis C, Edwards R, Faruque N, Feldman R, Gilbert J, Gilna P, Glöckner FO, Goldstein P, Guralnick R, Haft D, Hancock D, Hermjakob H, Hertz-Fowler C, Hugenholtz P, Joint I, Kagan L, Kane M, Kennedy J, Kowalchuk G, Kottmann R, Kolker E, Kravitz S, Kyrpides N, Leebens-Mack J, Lewis SE, Li K, Lister AL, Lord P, Maltsev N, Markowitz V, Martiny J, Methe B, Mizrachi I, Moxon R, Nelson K, Parkhill J, Proctor L, White O, Sansone S, Spiers A, Stevens R, Swift P, Taylor C, Tateno Y, Tett A, Turner S, Ussery D, Vaughan B, Ward N, Whetzel T, San Gil I, Wilson G, Wipat A: The minimum information about a genome sequence (MIGS) specification. Nat. Biotechnol 2008, 26:541-547. [PMID: 18464787]

  9. Breitbart M, Haynes M, Kelley S, Angly F, Edwards RA, Felts B, Mahaffy JM, Mueller J, Nulton J, Rayhawk S, Rodriguez-Brito B, Salamon P, Rohwer F: Viral diversity and dynamics in an infant gut. Res. Microbiol 2008, 159:367-373. [PMID: 18541415]

  10. Krause L, Diaz NN, Edwards RA, Gartemann K, Krömeke H, Neuweger H, Pühler A, Runte KJ, Schlüter A, Stoye J, Szczepanowski R, Tauch A, Goesmann A: Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor. J. Biotechnol 2008, 136:91-101. [PMID: 18611419]

  11. Marhaver KL, Edwards RA, Rohwer F: Viral communities associated with healthy and bleaching corals. Environ. Microbiol 2008, 10:2277-2286. [PMID: 18479440]

  12. Vega Thurber RL, Barott KL, Hall D, Liu H, Rodriguez-Mueller B, Desnues C, Edwards RA, Haynes M, Angly FE, Wegley L, Rohwer FL: Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa. Proc. Natl. Acad. Sci. U.S.A 2008, 105:18413-18418. [PMID: 19017800]

  13. Edwards, RA. 2008. The smallest cells pose the biggest problems: High Performance Computing and the Analysis of Metagenome Sequence Data. J. Phys. Conf Ser. 125:012050 [Google scholar]

  14. Meyer, F. Paarmann, D., D’Souza, M., Olson, R.D., Glass, E.M., Kubal, M., Paczian, T., Rodriguez, A., Stevens, R., Wilke, A., Wilkening, J. and R.A. Edwards. 2008. The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9:386 [PMID: 18803844]

  15. Gilbert, J.A., Field, D., Huang, Y., Edwards, R., Li, W., Gilna, P., and I. Joint. 2008. Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities. PLoS ONE 3(8): e3042 [PMID: 18725995]

  16. Wu, W., Edwards, R.A., Judson, I. R., Papka, M. E., Thomas, M., and Stevens, R. 2008. TeraGrid Open Life Science Gateway. Proceedings of the 3rd annual TeraGrid Conference, TeraGrid ’08.


2007

  1. Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Res. 2007 [PMID: 17690205]
    Edwards, R.A. and Dinsdale, E.A.. Marine Environmental Genomics: Unlocking the Ocean’s Secrets. Oceanography. 2007; 20:56-61. 2009
    Wegley L, Edwards R, Rodriguez-Brito B, Liu H, Rohwer F. Metagenomic analysis of the microbial community associated with the coral Porites astreoides. Environ Microbiol. 2007 [PMID: 17922755
    McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes S, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman A, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko O, Xia F, Zinner J, Overbeek R, Stevens R. The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. Nucleic Acids Res. 2007 [PMID: 17145713]

    Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Res. 2007 [PMID: 17690205]

  2. Edwards, R.A. and Dinsdale, E.A.. Marine Environmental Genomics: Unlocking the Ocean’s Secrets. Oceanography. 2007; 20:56-61.

  3. Wegley L, Edwards R, Rodriguez-Brito B, Liu H, Rohwer F. Metagenomic analysis of the microbial community associated with the coral Porites astreoides. Environ Microbiol. 2007 [PMID: 17922755]

  4. McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes S, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman A, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko O, Xia F, Zinner J, Overbeek R, Stevens R. The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. Nucleic Acids Res. 2007 [PMID: 17145713]

  5. Fierer N, Breitbart M, Nulton J, Salamon P, Lozupone C, Jones R, Robeson M, Edwards RA, Felts B, Rayhawk S. Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Applied and Environmental Microbiology 2007. [PMID: 17827313]

Making Android Videos

Since I agonized over how to make these videos both times I did it, I thought I’d write up a guide. I’ll assume that readers have already developed an Android application (or whatever else they want to take video of) and know how to run it for display.

To capture the video, I reccomend using Ubuntu and downloading gtk-recordMyDesktop. All of the mac/windows utilities I’ve found are paid and while some (read: Fraps) are pretty reasonably priced for the quality of the tool, free is always nice. Gtk will also record screen regions easily, which is ideal if, like me, you only want a portion of your screen recorded. In my case, I draw the record region around the mock cell phone displayed by the Android emulator. The program will output a .ogv file when recording is done.

To get this file into a format that your video editing software will care about, you have to do a little file format dance as follows. Open a terminal window. Write: ffmpeg -i inputFileName -b 5000k outputFileName.desiredFormat  (inputFileName is your output file from gtk. outputFileName is what you want the transcoder to spit out at the end. desiredFormat is .mov if you’re using iMovie.)

I’d like to note that I didn’t come up with that nice command-line jutsu on my own. I found it after Googling around for a while. I’m not entirely sure what all of those flags are for as I didn’t actually read the man page on ffmpeg.

Next, boot up your mac or whatever, transfer the files over, and edit away! Happy movie making!