| { |
| "v1_Abstract": "The Galaxy Project offers the popular web browser-based platform Galaxy for running bioinformatics tools and constructing simple workflows. Here, we present a broad collection of additional Galaxy tools for large scale analysis of gene and protein sequences. The motivating research theme is the identification of specific genes of interest in a range of nonmodel organisms, and our central example is the identification and prediction of \"effector\" proteins produced by plant pathogens in order to manipulate their host plant. This functional annotation of a pathogen's predicted capacity for virulence is a key step in translating sequence data into potential applications in plant pathology.", |
| "v2_Abstract": "The Galaxy Project offers the popular web browser-based platform Galaxy for running bioinformatics tools and constructing simple workflows. Here, we present a broad collection of additional Galaxy tools for large scale analysis of gene and protein sequences. This collection includes novel tools, wrappers for widely-used third-party tools such as NCBI BLAST+, and workflows that combine several existing tools to enable more complex analyses. Individual bioinformatics software tools (e.g. BLAST) are typically available separately as standalone packages, or in online browser-based form. However, organism scale analyses often require automation, and a corresponding bioinformatic skill set that includes familiarity with command line tools and scripting. The Galaxy framework enables the user to combine these same tools without demanding the same level of computing skill. Workflows created using Galaxy can be saved and are reusable, so may be distributed within and between research groups, facilitating the construction of a set of standardised, reusable bioinformatic protocols. The motivating research theme is the identification of specific genes of interest in a range of non-model organisms, and our central example is the identification and prediction of \"effector\" proteins produced by plant pathogens in order to manipulate their host plant. This functional annotation of a pathogen's predicted capacity for virulence is a key step in translating sequence data into potential applications in plant pathology. The Galaxy tools and workflows described in this manuscript are open source and freely available from the Galaxy Tool Shed (http://usegalaxy.org/toolshed or http://toolshed.g2.bx.psu.edu).", |
| "url": "https://peerj.com/articles/169/reviews/", |
| "review_1": "Michael Somers \u00b7 Aug 31, 2013 \u00b7 Academic Editor\nACCEPT\nThank you for the rvision. The MSreads well.", |
| "review_2": "Michael Somers \u00b7 Aug 23, 2013 \u00b7 Academic Editor\nMINOR REVISIONS\nI have read the MS and find it well written and almost ready for acceptance. Please consider the minor issues as given by the referees.", |
| "review_3": "Reviewer 1 \u00b7 Aug 15, 2013\nBasic reporting\nNo comments\nExperimental design\nThis manuscript by Higley and Brosius is well written and presents a well- designed study of a rare tiger beetle that has important implications for its conservation. The introduction presents the relevant literature and an effective background to this study. The data presented and the statistical analysis of these behaviors seems appropriate in providing valid evidence of difference among species.\nValidity of the findings\nThe conclusion that these determined differences in behavior can reduce competition for food seems well supported and justified. The different behaviors of C. n. lincolniana provide a valid insight to its adaptation to the saline habitats where it is found, and can inform management by protecting habitat with seeps and other features it requires\nAdditional comments\nI would offer an alternate or complementary explanation for the foraging microhabitat of togata. It is significantly smaller than the other species, with long legs and consequently can both extend higher above the substrate where it is slightly cooler and would have reduced heat loading and quicker cooling. In tiger beetles (and other insects) smaller body size can result is more effective behavioral thermoregulation that species with larger body size, thus allowing for foraging on warmer substrates or during the warmer parts of the day (Pearson and Vogler).\nCite this review as\nAnonymous Reviewer (2013) Peer Review #1 of \"Behavioral niche partitioning in a sympatric tiger beetle assemblage and implications for the endangered Salt Creek tiger beetle (v0.1)\". PeerJ https://doi.org/10.7287/peerj.169v0.1/reviews/1", |
| "review_4": "Reviewer 2 \u00b7 Jul 26, 2013\nBasic reporting\nThe authors introduce a very complex set of interactions in an understandable context of ecology and conservation. The English is solid with a minimum of unnecessary jargon. A simple but significant change should be made in lines 59 and 61. The endangered tiger beetle is not an endangered species. It is an endangered population or recognized subspecies. There are a few typos throughout (e.g., line 339 \"on\" should be inserted between reliance and shallow).\nExperimental design\nNo comments\nValidity of the findings\nNo comments\nAdditional comments\nThe authors successfully integrate a complex set of interactions and test them convincingly to accomplish both goals of ecology and conservation.\nCite this review as\nAnonymous Reviewer (2013) Peer Review #2 of \"Behavioral niche partitioning in a sympatric tiger beetle assemblage and implications for the endangered Salt Creek tiger beetle (v0.1)\". PeerJ https://doi.org/10.7287/peerj.169v0.1/reviews/2", |
| "pdf_1": "https://peerj.com/articles/169v0.2/submission", |
| "pdf_2": "https://peerj.com/articles/169v0.1/submission", |
| "all_reviews": "Review 1: Michael Somers \u00b7 Aug 31, 2013 \u00b7 Academic Editor\nACCEPT\nThank you for the rvision. The MSreads well.\nReview 2: Michael Somers \u00b7 Aug 23, 2013 \u00b7 Academic Editor\nMINOR REVISIONS\nI have read the MS and find it well written and almost ready for acceptance. Please consider the minor issues as given by the referees.\nReview 3: Reviewer 1 \u00b7 Aug 15, 2013\nBasic reporting\nNo comments\nExperimental design\nThis manuscript by Higley and Brosius is well written and presents a well- designed study of a rare tiger beetle that has important implications for its conservation. The introduction presents the relevant literature and an effective background to this study. The data presented and the statistical analysis of these behaviors seems appropriate in providing valid evidence of difference among species.\nValidity of the findings\nThe conclusion that these determined differences in behavior can reduce competition for food seems well supported and justified. The different behaviors of C. n. lincolniana provide a valid insight to its adaptation to the saline habitats where it is found, and can inform management by protecting habitat with seeps and other features it requires\nAdditional comments\nI would offer an alternate or complementary explanation for the foraging microhabitat of togata. It is significantly smaller than the other species, with long legs and consequently can both extend higher above the substrate where it is slightly cooler and would have reduced heat loading and quicker cooling. In tiger beetles (and other insects) smaller body size can result is more effective behavioral thermoregulation that species with larger body size, thus allowing for foraging on warmer substrates or during the warmer parts of the day (Pearson and Vogler).\nCite this review as\nAnonymous Reviewer (2013) Peer Review #1 of \"Behavioral niche partitioning in a sympatric tiger beetle assemblage and implications for the endangered Salt Creek tiger beetle (v0.1)\". PeerJ https://doi.org/10.7287/peerj.169v0.1/reviews/1\nReview 4: Reviewer 2 \u00b7 Jul 26, 2013\nBasic reporting\nThe authors introduce a very complex set of interactions in an understandable context of ecology and conservation. The English is solid with a minimum of unnecessary jargon. A simple but significant change should be made in lines 59 and 61. The endangered tiger beetle is not an endangered species. It is an endangered population or recognized subspecies. There are a few typos throughout (e.g., line 339 \"on\" should be inserted between reliance and shallow).\nExperimental design\nNo comments\nValidity of the findings\nNo comments\nAdditional comments\nThe authors successfully integrate a complex set of interactions and test them convincingly to accomplish both goals of ecology and conservation.\nCite this review as\nAnonymous Reviewer (2013) Peer Review #2 of \"Behavioral niche partitioning in a sympatric tiger beetle assemblage and implications for the endangered Salt Creek tiger beetle (v0.1)\". PeerJ https://doi.org/10.7287/peerj.169v0.1/reviews/2\nReview 5: nan\nReview 6: \n", |
| "LLM_extracted_review": "['Review 1: The manuscript reads well.\\n\\nReview 2: The manuscript is well written and almost ready for acceptance, but minor issues need to be addressed.\\n\\nReview 3: The study presents a well-designed investigation of a rare tiger beetle with important conservation implications. The introduction effectively covers relevant literature, and the statistical analysis supports the findings. An alternate explanation for the foraging microhabitat of togata is suggested, highlighting the advantages of smaller body size in behavioral thermoregulation.\\n\\nReview 4: The authors present a complex set of ecological interactions in an understandable manner. The English is solid, but a significant change is needed regarding the classification of the endangered tiger beetle. There are a few typos that should be corrected. The authors successfully integrate and test complex interactions for ecological and conservation goals.']" |
| } |
