Scientific Computing at NCEAS
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1 Scientific Computing at NCEAS Jim Regetz & Rick Reeves National Center for Ecological Analysis & Synthesis Winter Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
2 NCEAS Scientific Computing team Who we are... Rick Reeves: Geography, spatial data processing/analysis Jim Regetz: Ecology, statistics, numerical modeling Where you can find us... Office: Rm 301 (by the elevators) Web: Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
3 NCEAS technology support areas Collaboration Analysis Data & Metadata Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
4 Synthesis is an uphill battle Discovery Integration Analysis Publication The literature is the final resting place for much of our knowledge. Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
5 Synthesis is an uphill battle Discovery Integration Analysis Publication The literature is the final resting place for much of our knowledge. Data synthesis and re-analysis are hard in a publication-driven world! Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
6 NCEAS recycles! Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
7 Collaboration tools and services Tech support available on site Networking Printing Laptops Lab computers Video conferencing Smartboards Remote collaboration Password-protected group website Analytical server, source code repository, and more NCEAS Help Wiki: Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
8 Collaboration tools and services Tech support available on site Networking Printing Laptops Lab computers Video conferencing Smartboards Remote collaboration Password-protected group website Analytical server, source code repository, and more NCEAS Help Wiki: Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
9 Analysis support Data discovery & acquisition Consult with us about base layer data (e.g., global climate, digital terrain models) Data management & analysis Recommend best practices and appropriate software Discuss statistical & analytical approaches Lend a hand with programming, etc. Documentation & archiving How/where can you capture your analytical procedures? How/where can you archive data products? Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
10 Analysis support Data discovery & acquisition Consult with us about base layer data (e.g., global climate, digital terrain models) Data management & analysis Recommend best practices and appropriate software Discuss statistical & analytical approaches Lend a hand with programming, etc. Documentation & archiving How/where can you capture your analytical procedures? How/where can you archive data products? Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
11 Analysis support Data discovery & acquisition Consult with us about base layer data (e.g., global climate, digital terrain models) Data management & analysis Recommend best practices and appropriate software Discuss statistical & analytical approaches Lend a hand with programming, etc. Documentation & archiving How/where can you capture your analytical procedures? How/where can you archive data products? Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
12 Analytical software comparison Flexible Scripted Reliable Cross-platform Open source R x x x x x x Matlab x x x x SAS x x x x Free! Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
13 Analytical software comparison Flexible Scripted Reliable Cross-platform Open source R x x x x x x Matlab x x x x SAS x x x x Free! GRASS x x x x x x PostGIS x x x x x x ArcGIS x x x Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
14 Analytical software comparison Flexible Scripted Reliable Cross-platform Open source Free! R x x x x x x Matlab x x x x SAS x x x x Excel GRASS x x x x x x PostGIS x x x x x x ArcGIS x x x Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
15 Analytical software comparison Flexible Scripted Reliable Cross-platform Open source Free! R x x x x x x Matlab x x x x SAS x x x x Excel GRASS x x x x x x PostGIS x x x x x x ArcGIS x x x Also: C/C++, Python, Perl etc.; specialty apps upon request Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
16 Your responsibilities 1 Identify a Data Point of Contact for your group 2 Establish a timetable for documenting/archiving data 3 Create metadata entries in the NCEAS Data Repository for your data sets - as soon as possible! 4 Archive completed data sets in the Data Repository NCEAS Data Repository Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
17 Your responsibilities 1 Identify a Data Point of Contact for your group 2 Establish a timetable for documenting/archiving data 3 Create metadata entries in the NCEAS Data Repository for your data sets - as soon as possible! 4 Archive completed data sets in the Data Repository NCEAS Data Repository Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
18 Your responsibilities 1 Identify a Data Point of Contact for your group 2 Establish a timetable for documenting/archiving data 3 Create metadata entries in the NCEAS Data Repository for your data sets - as soon as possible! 4 Archive completed data sets in the Data Repository NCEAS Data Repository Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
19 Your responsibilities 1 Identify a Data Point of Contact for your group 2 Establish a timetable for documenting/archiving data 3 Create metadata entries in the NCEAS Data Repository for your data sets - as soon as possible! 4 Archive completed data sets in the Data Repository NCEAS Data Repository Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
20 NCEAS Ecoinformatics program Research Tools & services Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
21 NCEAS Ecoinformatics program Research Better managing heterogeneous data Capturing reproducible scientific workflows Interpreting data/analyses using semantic technologies Tools & services Metadata standard for scientific data (EML) Online repository for ecological data/metadata (KNB) Advanced storage system for data/metadata (Metacat) Desktop software for managing metadata (Morpho) Distributed scientific workflow platform (Kepler) Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
22 NCEAS Ecoinformatics program Research Better managing heterogeneous data Capturing reproducible scientific workflows Interpreting data/analyses using semantic technologies Tools & services Metadata standard for scientific data (EML) Online repository for ecological data/metadata (KNB) Advanced storage system for data/metadata (Metacat) Desktop software for managing metadata (Morpho) Distributed scientific workflow platform (Kepler) Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
23 Real world data vary in format, structure, semantics How do we deal with this heterogeneity? Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
24 Let data vary, but formalize metadata Metadata makes data useful Needed to assess/interpret data Provides critical context Owner, Abstract, Methods Variables, Sites, Units Ecological Metadata Language (EML) Metadata standard: rules about what and how to say things Developed by scientists, for scientists Human-readable, yet machine-interpretable Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
25 Let data vary, but formalize metadata Metadata makes data useful Needed to assess/interpret data Provides critical context Owner, Abstract, Methods Variables, Sites, Units Ecological Metadata Language (EML) Metadata standard: rules about what and how to say things Developed by scientists, for scientists Human-readable, yet machine-interpretable Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
26 Data documentation made easy Basic option: Web upload Simple online form General metadata only Upload data files Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
27 Data documentation made easy Basic option: Web upload Simple online form General metadata only Upload data files Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
28 Data documentation made easy Basic option: Web upload Simple online form General metadata only Upload data files Advanced option: Install Morpho desktop software (free!) Create & save detailed metadata using wizards 1 Manage your data on your own computer 2 Share with specific colleagues: set access priveleges 3 Share metadata/data with entire community Search and locate data and metadata on the network Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
29 Morpho: View data table descriptions Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
30 Search online ( Participants NCEAS LTER OBFS PISCO ESA UCNRS SANParks TERN... and more Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
31 Thanks for listening... Questions? Jim Regetz & Rick Reeves (NCEAS) Scientific Computing Overview Winter / 16
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