More Like this

1. NEON Tree Crowns Dataset

   https://doi.org/10.5281/zenodo.3765871  

   Weinstein, Ben; Marconi, Sergio; Zare, Alina; Bohlman, Stephanie; Graves, Sarah; Singh, Aditya; White, Ethan (January 2020, Zenodo)

   {"Abstract":["Abstract<\/strong><\/p>\n\nThe NeonTreeCrowns dataset is a set of individual level crown estimates for 100 million trees at 37 geographic sites across the United States surveyed by the National Ecological Observation Network\u2019s Airborne Observation Platform. Each rectangular bounding box crown prediction includes height, crown area, and spatial location. <\/p>\n\nHow can I see the data?<\/strong><\/p>\n\nA web server to look through predictions is available through idtrees.org<\/p>\n\nDataset Organization<\/strong><\/p>\n\nThe shapefiles.zip contains 11,000 shapefiles, each corresponding to a 1km^2 RGB tile from NEON (ID: DP3.30010.001). For example "2019_SOAP_4_302000_4100000_image.shp" are the predictions from "2019_SOAP_4_302000_4100000_image.tif" available from the NEON data portal: https://data.neonscience.org/data-products/explore?search=camera. NEON's file convention refers to the year of data collection (2019), the four letter site code (SOAP), the sampling event (4), and the utm coordinate of the top left corner (302000_4100000). For NEON site abbreviations and utm zones see https://www.neonscience.org/field-sites/field-sites-map. <\/p>\n\nThe predictions are also available as a single csv for each file. All available tiles for that site and year are combined into one large site. These data are not projected, but contain the utm coordinates for each bounding box (left, bottom, right, top). For both file types the following fields are available:<\/p>\n\nHeight: The crown height measured in meters. Crown height is defined as the 99th quartile of all canopy height pixels from a LiDAR height model (ID: DP3.30015.001)<\/p>\n\nArea: The crown area in m^{2<\/sup> of the rectangular bounding box.<\/p>\n\n}Label: All data in this release are "Tree".<\/p>\n\nScore: The confidence score from the DeepForest deep learning algorithm. The score ranges from 0 (low confidence) to 1 (high confidence)<\/p>\n\nHow were predictions made?<\/strong><\/p>\n\nThe DeepForest algorithm is available as a python package: https://deepforest.readthedocs.io/. Predictions were overlaid on the LiDAR-derived canopy height model. Predictions with heights less than 3m were removed.<\/p>\n\nHow were predictions validated?<\/strong><\/p>\n\nPlease see<\/p>\n\nWeinstein, B. G., Marconi, S., Bohlman, S. A., Zare, A., & White, E. P. (2020). Cross-site learning in deep learning RGB tree crown detection. Ecological Informatics<\/em>, 56<\/em>, 101061.<\/p>\n\nWeinstein, B., Marconi, S., Aubry-Kientz, M., Vincent, G., Senyondo, H., & White, E. (2020). DeepForest: A Python package for RGB deep learning tree crown delineation. bioRxiv<\/em>.<\/p>\n\nWeinstein, Ben G., et al. "Individual tree-crown detection in RGB imagery using semi-supervised deep learning neural networks." Remote Sensing<\/em> 11.11 (2019): 1309.<\/p>\n\nWere any sites removed?<\/strong><\/p>\n\nSeveral sites were removed due to poor NEON data quality. GRSM and PUUM both had lower quality RGB data that made them unsuitable for prediction. NEON surveys are updated annually and we expect future flights to correct these errors. We removed the GUIL puerto rico site due to its very steep topography and poor sunangle during data collection. The DeepForest algorithm responded poorly to predicting crowns in intensely shaded areas where there was very little sun penetration. We are happy to make these data are available upon request.<\/p>\n\n# Contact<\/p>\n\nWe welcome questions, ideas and general inquiries. The data can be used for many applications and we look forward to hearing from you. Contact ben.weinstein@weecology.org. <\/p>"],"Other":["Gordon and Betty Moore Foundation: GBMF4563"]} 

   more » « less
2. UC Santa Barbara Invertebrate Zoology Collection (UCSB-IZC) Data Archive and Biodiversity Dataset Graph

   https://doi.org/10.5281/zenodo.5660088  

   Cheadle Center for Biodiversity and Ecological Restoration, University of (January 2021, Zenodo)

   {"Abstract":["A biodiversity dataset graph: UCSB-IZC<\/p>\n\nThe intended use of this archive is to facilitate (meta-)analysis of the UC Santa Barbara Invertebrate Zoology Collection (UCSB-IZC). UCSB-IZC is a natural history collection of invertebrate zoology at Cheadle Center of Biodiversity and Ecological Restoration, University of California Santa Barbara.<\/p>\n\nThis dataset provides versioned snapshots of the UCSB-IZC network as tracked by Preston [2,3] between 2021-10-08 and 2021-11-04 using [preston track "https://api.gbif.org/v1/occurrence/search/?datasetKey=d6097f75-f99e-4c2a-b8a5-b0fc213ecbd0"].<\/p>\n\nThis archive contains 14349 images related to 32533 occurrence/specimen records. See included sample-image.jpg and their associated meta-data sample-image.json [4].<\/p>\n\nThe images were counted using:<\/p>\n\n$$ preston cat hash://sha256/80c0f5fc598be1446d23c95141e87880c9e53773cb2e0b5b54cb57a8ea00b20c\\\n | grep -o -P ".*depict"\\\n | sort\\\n | uniq\\\n | wc -l<\/p>\n\nAnd the occurrences were counted using:<\/p>\n\n$$ preston cat hash://sha256/80c0f5fc598be1446d23c95141e87880c9e53773cb2e0b5b54cb57a8ea00b20c\\\n | grep -o -P "occurrence/([0-9])+"\\\n | sort\\\n | uniq\\\n | wc -l<\/p>\n\nThe archive consists of 256 individual parts (e.g., preston-00.tar.gz, preston-01.tar.gz, ...) to allow for parallel file downloads. The archive contains three types of files: index files, provenance files and data files. Only two index and provenance files are included and have been individually included in this dataset publication. Index files provide a way to links provenance files in time to establish a versioning mechanism.<\/p>\n\nTo retrieve and verify the downloaded UCSB-IZC biodiversity dataset graph, first download preston-*.tar.gz. Then, extract the archives into a "data" folder. Alternatively, you can use the Preston [2,3] command-line tool to "clone" this dataset using:<\/p>\n\n$$ java -jar preston.jar clone --remote https://archive.org/download/preston-ucsb-izc/data.zip/,https://zenodo.org/record/5557670/files,https://zenodo.org/record/5557670/files/5660088<\/p>\n\nAfter that, verify the index of the archive by reproducing the following provenance log history:<\/p>\n\n$$ java -jar preston.jar history\n<urn:uuid:0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/pav/hasVersion> <hash://sha256/d5eb492d3e0304afadcc85f968de1e23042479ad670a5819cee00f2c2c277f36> .\n<hash://sha256/80c0f5fc598be1446d23c95141e87880c9e53773cb2e0b5b54cb57a8ea00b20c> <http://purl.org/pav/previousVersion> <hash://sha256/d5eb492d3e0304afadcc85f968de1e23042479ad670a5819cee00f2c2c277f36> .<\/p>\n\nTo check the integrity of the extracted archive, confirm that each line produce by the command "preston verify" produces lines as shown below, with each line including "CONTENT_PRESENT_VALID_HASH". Depending on hardware capacity, this may take a while.<\/p>\n\n$ java -jar preston.jar verify\nhash://sha256/ce1dc2468dfb1706a6f972f11b5489dc635bdcf9c9fd62a942af14898c488b2c    file:/home/jhpoelen/ucsb-izc/data/ce/1d/ce1dc2468dfb1706a6f972f11b5489dc635bdcf9c9fd62a942af14898c488b2c    OK    CONTENT_PRESENT_VALID_HASH    66438    hash://sha256/ce1dc2468dfb1706a6f972f11b5489dc635bdcf9c9fd62a942af14898c488b2c\nhash://sha256/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844    file:/home/jhpoelen/ucsb-izc/data/f6/8d/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844    OK    CONTENT_PRESENT_VALID_HASH    4093    hash://sha256/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844\nhash://sha256/3e70b7adc1a342e5551b598d732c20b96a0102bb1e7f42cfc2ae8a2c4227edef    file:/home/jhpoelen/ucsb-izc/data/3e/70/3e70b7adc1a342e5551b598d732c20b96a0102bb1e7f42cfc2ae8a2c4227edef    OK    CONTENT_PRESENT_VALID_HASH    5746    hash://sha256/3e70b7adc1a342e5551b598d732c20b96a0102bb1e7f42cfc2ae8a2c4227edef\nhash://sha256/995806159ae2fdffdc35eef2a7eccf362cb663522c308aa6aa52e2faca8bb25b    file:/home/jhpoelen/ucsb-izc/data/99/58/995806159ae2fdffdc35eef2a7eccf362cb663522c308aa6aa52e2faca8bb25b    OK    CONTENT_PRESENT_VALID_HASH    6147    hash://sha256/995806159ae2fdffdc35eef2a7eccf362cb663522c308aa6aa52e2faca8bb25b<\/p>\n\nNote that a copy of the java program "preston", preston.jar, is included in this publication. The program runs on java 8+ virtual machine using "java -jar preston.jar", or in short "preston".<\/p>\n\nFiles in this data publication:<\/p>\n\n--- start of file descriptions ---<\/p>\n\n-- description of archive and its contents (this file) --\nREADME<\/p>\n\n-- executable java jar containing preston [2,3] v0.3.1. --\npreston.jar<\/p>\n\n-- preston archive containing UCSB-IZC (meta-)data/image files, associated provenance logs and a provenance index --\npreston-[00-ff].tar.gz<\/p>\n\n-- individual provenance index files --\n2a5de79372318317a382ea9a2cef069780b852b01210ef59e06b640a3539cb5a<\/p>\n\n-- example image and meta-data --\nsample-image.jpg (with hash://sha256/916ba5dc6ad37a3c16634e1a0e3d2a09969f2527bb207220e3dbdbcf4d6b810c)\nsample-image.json (with hash://sha256/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844)<\/p>\n\n--- end of file descriptions ---<\/p>\n\n\nReferences<\/p>\n\n[1] Cheadle Center for Biodiversity and Ecological Restoration (2021). University of California Santa Barbara Invertebrate Zoology Collection. Occurrence dataset https://doi.org/10.15468/w6hvhv accessed via GBIF.org on 2021-11-04 as indexed by the Global Biodiversity Informatics Facility (GBIF) with provenance hash://sha256/d5eb492d3e0304afadcc85f968de1e23042479ad670a5819cee00f2c2c277f36 hash://sha256/80c0f5fc598be1446d23c95141e87880c9e53773cb2e0b5b54cb57a8ea00b20c.\n[2] https://preston.guoda.bio, https://doi.org/10.5281/zenodo.1410543 .\n[3] MJ Elliott, JH Poelen, JAB Fortes (2020). Toward Reliable Biodiversity Dataset References. Ecological Informatics. https://doi.org/10.1016/j.ecoinf.2020.101132\n[4] Cheadle Center for Biodiversity and Ecological Restoration (2021). University of California Santa Barbara Invertebrate Zoology Collection. Occurrence dataset https://doi.org/10.15468/w6hvhv accessed via GBIF.org on 2021-10-08. https://www.gbif.org/occurrence/3323647301 . hash://sha256/f68d489a9275cb9d1249767244b594c09ab23fd00b82374cb5877cabaa4d0844 hash://sha256/916ba5dc6ad37a3c16634e1a0e3d2a09969f2527bb207220e3dbdbcf4d6b810c<\/p>"],"Other":["This work is funded in part by grant NSF OAC 1839201 and NSF DBI 2102006 from the National Science Foundation."]} 

   more » « less
3. MELNHE: Foliar Chemistry 2008-2016 in Bartlett, Hubbard Brook, and Jeffers Brook (12 stands)

   https://doi.org/10.6073/pasta/b23deb8e1ccf1c1413382bf911c6be19  

   Hong, Sunghoon D; Gonzales, Kara E; See, Craig R; Yanai, Ruth D (January 2021, Environmental Data Initiative)

   We are conducting nutrient manipulations in three study sites in the White Mountain National Forest in New Hampshire: Bartlett Experimental Forest, Hubbard Brook Experimental Forest, and Jeffers Brook. We monitored foliar chemistry in 12 of our stands (excluding C3) pre-treatment (2008-2010) and post-treatment (2014-2016). In general, we found that foliar N concentrations were higher with N addition and foliar P concentrations were higher with P addition. More interestingly, P addition reduced foliar N concentrations and N addition reduced foliar P concentrations. Some interactive effects were observed (i.e. NxP, Species x N, Species x P, Species x N x P). This dataset contains pre- and post- treatment foliar chemistry data, and data from the analysis of quality control standard samples. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station. 

   more » « less
4. A biodiversity dataset graph: Biodiverity Heritage Library (BHL)

   https://doi.org/10.5281/zenodo.3849560  

   Poelen, Jorrit (January 2020, Zenodo)

   {"Abstract":["A biodiversity dataset graph: BHL<\/p>\n\nThe intended use of this archive is to facilitate (meta-)analysis of the Biodiversity Heritage Library (BHL). The Biodiversity Heritage Library improves research methodology by collaboratively making biodiversity literature openly available to the world as part of a global biodiversity community.<\/p>\n\nThis dataset provides versioned snapshots of the BHL network as tracked by Preston [2] between 2019-05-19 and 2020-05-09 using "preston update -u https://biodiversitylibrary.org".<\/p>\n\nThe archive consists of 256 individual parts (e.g., preston-00.tar.gz, preston-01.tar.gz, ...) to allow for parallel file downloads. The archive contains three types of files: index files, provenance logs and data files. In addition, index files have been individually included in this dataset publication to facilitate remote access. Index files provide a way to links provenance files in time to establish a versioning mechanism. Provenance files describe how, when, what and where the BHL content was retrieved. For more information, please visit https://preston.guoda.bio or https://doi.org/10.5281/zenodo.1410543 .  <\/p>\n\nTo retrieve and verify the downloaded BHL biodiversity dataset graph, first concatenate all the downloaded preston-*.tar.gz files (e.g., cat preston-*.tar.gz > preston.tar.gz). Then, extract the archives into a "data" folder. Alternatively, you can use the preston[2] command-line tool to "clone" this dataset using:<\/p>\n\n$$ java -jar preston.jar clone --remote https://zenodo.org/record/3849560/files<\/p>\n\nAfter that, verify the index of the archive by reproducing the following provenance log history:<\/p>\n\n$$ java -jar preston.jar history\n<0659a54f-b713-4f86-a917-5be166a14110> <http://purl.org/pav/hasVersion> <hash://sha256/89926f33157c0ef057b6de73f6c8be0060353887b47db251bfd28222f2fd801a> .\n<hash://sha256/41b19aa9456fc709de1d09d7a59c87253bc1f86b68289024b7320cef78b3e3a4> <http://purl.org/pav/previousVersion> <hash://sha256/89926f33157c0ef057b6de73f6c8be0060353887b47db251bfd28222f2fd801a> .\n<hash://sha256/7582d5ba23e0d498ca4f55c29408c477d0d92b4fdcea139e8666f4d78c78a525> <http://purl.org/pav/previousVersion> <hash://sha256/41b19aa9456fc709de1d09d7a59c87253bc1f86b68289024b7320cef78b3e3a4> .\n<hash://sha256/a70774061ccded1a45389b9e6063eb3abab3d42813aa812391f98594e7e26687> <http://purl.org/pav/previousVersion> <hash://sha256/7582d5ba23e0d498ca4f55c29408c477d0d92b4fdcea139e8666f4d78c78a525> .\n<hash://sha256/007e065ba4b99867751d688754aa3d33fa96e6e03133a2097e8a368d613cd93a> <http://purl.org/pav/previousVersion> <hash://sha256/a70774061ccded1a45389b9e6063eb3abab3d42813aa812391f98594e7e26687> .\n<hash://sha256/4fb4b4d8f1ae2961311fb0080e817adb2faa746e7eae15249a3772fbe2d662a1> <http://purl.org/pav/previousVersion> <hash://sha256/007e065ba4b99867751d688754aa3d33fa96e6e03133a2097e8a368d613cd93a> .\n<hash://sha256/67cc329e74fd669945f503917fbb942784915ab7810ddc41105a82ebe6af5482> <http://purl.org/pav/previousVersion> <hash://sha256/4fb4b4d8f1ae2961311fb0080e817adb2faa746e7eae15249a3772fbe2d662a1> .\n<hash://sha256/e46cd4b0d7fdb51ea789fa3c5f7b73591aca62d2d8f913346d71aa6cf0745c9f> <http://purl.org/pav/previousVersion> <hash://sha256/67cc329e74fd669945f503917fbb942784915ab7810ddc41105a82ebe6af5482> .\n<hash://sha256/9215d543418a80510e78d35a0cfd7939cc59f0143d81893ac455034b5e96150a> <http://purl.org/pav/previousVersion> <hash://sha256/e46cd4b0d7fdb51ea789fa3c5f7b73591aca62d2d8f913346d71aa6cf0745c9f> .\n<hash://sha256/1448656cc9f339b4911243d7c12f3ba5366b54fff3513640306682c50f13223d> <http://purl.org/pav/previousVersion> <hash://sha256/9215d543418a80510e78d35a0cfd7939cc59f0143d81893ac455034b5e96150a> .\n<hash://sha256/7ee6b16b7a5e9b364776427d740332d8552adf5041d48018eeb3c0e13ccebf27> <http://purl.org/pav/previousVersion> <hash://sha256/1448656cc9f339b4911243d7c12f3ba5366b54fff3513640306682c50f13223d> .\n<hash://sha256/34ccd7cf7f4a1ea35ac6ae26a458bb603b2f6ee8ad36e1a58aa0261105d630b1> <http://purl.org/pav/previousVersion> <hash://sha256/7ee6b16b7a5e9b364776427d740332d8552adf5041d48018eeb3c0e13ccebf27> .<\/p>\n\nTo check the integrity of the extracted archive, confirm that each line produce by the command "preston verify" produces lines as shown below, with each line including "CONTENT_PRESENT_VALID_HASH". Depending on hardware capacity, this may take a while.<\/p>\n\n$ java -jar preston.jar verify\nhash://sha256/e0c131ebf6ad2dce71ab9a10aa116dcedb219ae4539f9e5bf0e57b84f51f22ca    file:/home/preston/preston-bhl/data/e0/c1/e0c131ebf6ad2dce71ab9a10aa116dcedb219ae4539f9e5bf0e57b84f51f22ca    OK    CONTENT_PRESENT_VALID_HASH    49458087    hash://sha256/e0c131ebf6ad2dce71ab9a10aa116dcedb219ae4539f9e5bf0e57b84f51f22ca\nhash://sha256/1a57e55a780b86cff38697cf1b857751ab7b389973d35113564fe5a9a58d6a99    file:/home/preston/preston-bhl/data/1a/57/1a57e55a780b86cff38697cf1b857751ab7b389973d35113564fe5a9a58d6a99    OK    CONTENT_PRESENT_VALID_HASH    25745    hash://sha256/1a57e55a780b86cff38697cf1b857751ab7b389973d35113564fe5a9a58d6a99\nhash://sha256/85efeb84c1b9f5f45c7a106dd1b5de43a31b3248a211675441ff584a7154b61c    file:/home/preston/preston-bhl/data/85/ef/85efeb84c1b9f5f45c7a106dd1b5de43a31b3248a211675441ff584a7154b61c    OK    CONTENT_PRESENT_VALID_HASH    519892    hash://sha256/85efeb84c1b9f5f45c7a106dd1b5de43a31b3248a211675441ff584a7154b61c\nhash://sha256/251e5032afce4f1e44bfdc5a8f0316ca1b317e8af41bdbf88163ab5bd2b52743    file:/home/preston/preston-bhl/data/25/1e/251e5032afce4f1e44bfdc5a8f0316ca1b317e8af41bdbf88163ab5bd2b52743    OK    CONTENT_PRESENT_VALID_HASH    787414    hash://sha256/251e5032afce4f1e44bfdc5a8f0316ca1b317e8af41bdbf88163ab5bd2b52743<\/p>\n\nNote that a copy of the java program "preston", preston.jar, is included in this publication. The program runs on java 8+ virtual machine using "java -jar preston.jar", or in short "preston".<\/p>\n\nFiles in this data publication:<\/p>\n\n--- start of file descriptions ---<\/p>\n\n-- description of archive and its contents (this file) --\nREADME<\/p>\n\n-- executable java jar containing preston[2] v0.1.15. --\npreston.jar<\/p>\n\n-- preston archives containing BHL data files, associated provenance logs and a provenance index --\npreston-[00-ff].tar.gz<\/p>\n\n-- individual provenance index files --\n2a5de79372318317a382ea9a2cef069780b852b01210ef59e06b640a3539cb5a\n2b1104cb7749e818c9afca78391b2d0099bbb0a32f2b348860a335cd2f8f6800\n4081bc59dff58d63f6a86c623cb770f01e9a355a42495b205bcb538cd526190f\n47a2816f8b5600b24487093adcddfea12434cc4f270f3ab09d9215fbdd546cd2\n6f99a1388823fca745c9e22ac21e2da909a219aa1ace55170fa9248c0276903c\n7ae46d7cd9b5a0f5889ba38bac53c82e591b0bdf8b605f5e48c0dce8fb7b717f\n82903464889fea7c53f53daedf4e41fa31092f82619edeb3415eb2b473f74af3\n9e8c86243df39dd4fe82a3f814710eccf73aa9291d050415408e346fa2b09e70\na8308fbf4530e287927c471d881ce0fc852f16543d46e1ee26f1caba48815f3a\nbcec6df2ea7f74e9a6e2830d0072e6b2fbe65323d9ddb022dd6e1349c23996e2\ncfe47c25ec0210ac73c06b407beb20d9c58355cb15bae427fdc7541870ca2e4e\nf73fc9e70bce8f21f0c96b8ef0903749d8f223f71343ab5a8910968f99c9b8b6<\/p>\n\n--- end of file descriptions ---<\/p>\n\n\nReferences<\/p>\n\n[1] Biodiversity Heritage Library (BHL, https://biodiversitylibrary.org) accessed from 2019-05-19 to 2020-05-09 with provenance hash://sha256/34ccd7cf7f4a1ea35ac6ae26a458bb603b2f6ee8ad36e1a58aa0261105d630b1.\n[2] https://preston.guoda.bio, https://doi.org/10.5281/zenodo.1410543 .<\/p>\n\n\nThis work is funded in part by grant NSF OAC 1839201 from the National Science Foundation.<\/p>"]} 

   more » « less
5. Simulation Data for Design of Peptides that Fold and Self-Assemble on Graphite

   https://doi.org/10.5281/zenodo.6426152  

   Comer, Jeffrey; Thakkar, Ravindra; Velásquez-Silva, Astrid; Miranda-Carvajal, Ingrid (January 2022, Zenodo)

   {"Abstract":["This data set for the manuscript entitled "Design of Peptides that Fold and Self-Assemble on Graphite" includes all files needed to run and analyze the simulations described in the this manuscript in the molecular dynamics software NAMD, as well as the output of the simulations. The files are organized into directories corresponding to the figures of the main text and supporting information. They include molecular model structure files (NAMD psf or Amber prmtop format), force field parameter files (in CHARMM format), initial atomic coordinates (pdb format), NAMD configuration files, Colvars configuration files, NAMD log files, and NAMD output including restart files (in binary NAMD format) and trajectories in dcd format (downsampled to 10 ns per frame). Analysis is controlled by shell scripts (Bash-compatible) that call VMD Tcl scripts or python scripts. These scripts and their output are also included.<\/p>\n\nVersion: 2.0<\/p>\n\nChanges versus version 1.0 are the addition of the free energy of folding, adsorption, and pairing calculations (Sim_Figure-7) and shifting of the figure numbers to accommodate this addition.<\/p>\n\n\nConventions Used in These Files\n===============================<\/p>\n\nStructure Files\n----------------\n- graph_*.psf or sol_*.psf (original NAMD (XPLOR?) format psf file including atom details (type, charge, mass), as well as definitions of bonds, angles, dihedrals, and impropers for each dipeptide.)<\/p>\n\n- graph_*.pdb or sol_*.pdb (initial coordinates before equilibration)\n- repart_*.psf (same as the above psf files, but the masses of non-water hydrogen atoms have been repartitioned by VMD script repartitionMass.tcl)\n- freeTop_*.pdb (same as the above pdb files, but the carbons of the lower graphene layer have been placed at a single z value and marked for restraints in NAMD)\n- amber_*.prmtop (combined topology and parameter files for Amber force field simulations)\n- repart_amber_*.prmtop (same as the above prmtop files, but the masses of non-water hydrogen atoms have been repartitioned by ParmEd)<\/p>\n\nForce Field Parameters\n----------------------\nCHARMM format parameter files:\n- par_all36m_prot.prm (CHARMM36m FF for proteins)\n- par_all36_cgenff_no_nbfix.prm (CGenFF v4.4 for graphene) The NBFIX parameters are commented out since they are only needed for aromatic halogens and we use only the CG2R61 type for graphene.\n- toppar_water_ions_prot_cgenff.str (CHARMM water and ions with NBFIX parameters needed for protein and CGenFF included and others commented out)<\/p>\n\nTemplate NAMD Configuration Files\n---------------------------------\nThese contain the most commonly used simulation parameters. They are called by the other NAMD configuration files (which are in the namd/ subdirectory):\n- template_min.namd (minimization)\n- template_eq.namd (NPT equilibration with lower graphene fixed)\n- template_abf.namd (for adaptive biasing force)<\/p>\n\nMinimization\n-------------\n- namd/min_*.0.namd<\/p>\n\nEquilibration\n-------------\n- namd/eq_*.0.namd<\/p>\n\nAdaptive biasing force calculations\n-----------------------------------\n- namd/eabfZRest7_graph_chp1404.0.namd\n- namd/eabfZRest7_graph_chp1404.1.namd (continuation of eabfZRest7_graph_chp1404.0.namd)<\/p>\n\nLog Files\n---------\nFor each NAMD configuration file given in the last two sections, there is a log file with the same prefix, which gives the text output of NAMD. For instance, the output of namd/eabfZRest7_graph_chp1404.0.namd is eabfZRest7_graph_chp1404.0.log.<\/p>\n\nSimulation Output\n-----------------\nThe simulation output files (which match the names of the NAMD configuration files) are in the output/ directory. Files with the extensions .coor, .vel, and .xsc are coordinates in NAMD binary format, velocities in NAMD binary format, and extended system information (including cell size) in text format. Files with the extension .dcd give the trajectory of the atomic coorinates over time (and also include system cell information). Due to storage limitations, large DCD files have been omitted or replaced with new DCD files having the prefix stride50_ including only every 50 frames. The time between frames in these files is 50 * 50000 steps/frame * 4 fs/step = 10 ns. The system cell trajectory is also included for the NPT runs are output/eq_*.xst.<\/p>\n\nScripts\n-------\nFiles with the .sh extension can be found throughout. These usually provide the highest level control for submission of simulations and analysis. Look to these as a guide to what is happening. If there are scripts with step1_*.sh and step2_*.sh, they are intended to be run in order, with step1_*.sh first.<\/p>\n\n\nCONTENTS\n========<\/p>\n\nThe directory contents are as follows. The directories Sim_Figure-1 and Sim_Figure-8 include README.txt files that describe the files and naming conventions used throughout this data set.<\/p>\n\nSim_Figure-1: Simulations of N-acetylated C-amidated amino acids (Ac-X-NHMe) at the graphite\u2013water interface.<\/p>\n\nSim_Figure-2: Simulations of different peptide designs (including acyclic, disulfide cyclized, and N-to-C cyclized) at the graphite\u2013water interface.<\/p>\n\nSim_Figure-3: MM-GBSA calculations of different peptide sequences for a folded conformation and 5 misfolded/unfolded conformations.<\/p>\n\nSim_Figure-4: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite\u2013water interface at 370 K.<\/p>\n\nSim_Figure-5: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite\u2013water interface at 295 K.<\/p>\n\nSim_Figure-5_replica: Temperature replica exchange molecular dynamics simulations for the peptide cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) with 20 replicas for temperatures from 295 to 454 K.<\/p>\n\nSim_Figure-6: Simulation of the peptide molecule cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) in free solution (no graphite).<\/p>\n\nSim_Figure-7: Free energy calculations for folding, adsorption, and pairing for the peptide CHP1404 (sequence: cyc(GTGSGTG-GPGG-GCGTGTG-SGPG)). For folding, we calculate the PMF as function of RMSD by replica-exchange umbrella sampling (in the subdirectory Folding_CHP1404_Graphene/). We make the same calculation in solution, which required 3 seperate replica-exchange umbrella sampling calculations (in the subdirectory Folding_CHP1404_Solution/). Both PMF of RMSD calculations for the scrambled peptide are in Folding_scram1404/. For adsorption, calculation of the PMF for the orientational restraints and the calculation of the PMF along z (the distance between the graphene sheet and the center of mass of the peptide) are in Adsorption_CHP1404/ and Adsorption_scram1404/. The actual calculation of the free energy is done by a shell script ("doRestraintEnergyError.sh") in the 1_free_energy/ subsubdirectory. Processing of the PMFs must be done first in the 0_pmf/ subsubdirectory. Finally, files for free energy calculations of pair formation for CHP1404 are found in the Pair/ subdirectory.<\/p>\n\nSim_Figure-8: Simulation of four peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) where the peptides are far above the graphene\u2013water interface in the initial configuration.<\/p>\n\nSim_Figure-9: Two replicates of a simulation of nine peptide molecules with the sequence cyc(GTGSGTG-GPGG-GCGTGTG-SGPG) at the graphite\u2013water interface at 370 K.<\/p>\n\nSim_Figure-9_scrambled: Two replicates of a simulation of nine peptide molecules with the control sequence cyc(GGTPTTGGGGGGSGGPSGTGGC) at the graphite\u2013water interface at 370 K.<\/p>\n\nSim_Figure-10: Adaptive biasing for calculation of the free energy of the folded peptide as a function of the angle between its long axis and the zigzag directions of the underlying graphene sheet.<\/p>\n\n <\/p>"],"Other":["This material is based upon work supported by the US National Science Foundation under grant no. DMR-1945589. A majority of the computing for this project was performed on the Beocat Research Cluster at Kansas State University, which is funded in part by NSF grants CHE-1726332, CNS-1006860, EPS-1006860, and EPS-0919443. This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number ACI-1548562, through allocation BIO200030."]} 

   more » « less