Status

In LIFEPLAN we collect large amounts of samples and digital data. How do we get from samples to species lists, and where are we now?
Current status

Figure: Current status of the pipelines for different methods, October 10 2023. For all methods, we go from samples to species lists. For all methods, new samples are coming in all the time, and the current status refers to the status of the first samples. Malaise samples have sequencing, imaging and initial bioinformatics done, but we will be performing more full bioinformatics before making actual species lists. Cyclone samples are going through drying and cleaning, and the first samples are being sequenced. They will still need to go through the bioinformatics stage. Soil samples have been freeze dried and ground, and have started sequencing. They will still need to go through the bioinformatics stage. Camera trap data is uploading, and we now in the annotation phase. After annotation, we will perform automated species classification to arrive at species lists. Audio data is uploading, and we are currently in the annotation phase. After annotation, we will perform automated species classification to arrive at species lists.
Cyclone sampling

SLU = Swedish University of Agricultural Sciences in Uppsala

UH = University of Helsinki

JyU = Jyväskylä University

CBG = Centre for Biodiversity Genomics

 

  • Sample collection
    • Teams collect two weekly 24-hour samples
    • Teams create metadata by scanning QR codes on cyclone sampler and sample vial with Lifeplan app
    • Teams store samples until shipment in a freezer
       
  • Sample shipping to Sweden
    • Teams ship samples to Lifeplan SLU in Uppsala
    • Lifeplan SLU scans vials’ QR codes on arrival
    • Lifeplan UH checks up on any missing or confusing metadata with the team
       
  • Sample cleaning by Lifeplan
    • Lifeplan SLU cleans samples by removing any visible debris such as insects
    • Lifeplan SLU freeze dries the samples and stores them at -20 C
       
  • Sample shipping to Guelph
    • Lifeplan SLU selects one sample from each week and stores the other weekly sample as a backup
    • Lifeplan SLU ships the selected samples to Centre for Biodiversity Genomics (CBG) in Guelph along with metadata 
    • CBG scans vials on arrival and saves metadata
    • Lifeplan UH sends a copy of each team’s Material Transfer Agreement to Guelph to ensure that we have the right to process the samples, and determine whether eventual DNA extracts should be stored, destroyed or repatriated after analysis. 
       
  • Sample sequencing
  • Transfer of sequencing data to Lifeplan
    • CBG uploads raw sequencing data to their mBRAVE system, giving access to Lifeplan researchers. 
    • CBG sends raw sequencing data to Lifeplan UH as downloadable files. Lifeplan UH stores the data on ALLAS, giving access to Lifeplan researchers.
    • Transfer of sequencing data to teams to be announced soon
       
  • Bioinformatics
    • CBG performs initial bioinformatics with the mBRAVE system, where species assignments are based on matching sequences over a certain threshold.
    • Lifeplan UH/JyU/Duke performs bioinformatics with the PROTAX system, which is a probabilistic taxonomic classification software. It handles unknown taxa better than mBRAVE and gives probabilities to classifications.
       
  • Species lists
    • Lifeplan UH/JyU/Duke translates PROTAX results into species-by-sample matrices: lists of which species were found in which samples.
    • Lifeplan UH sends species lists to the teams as they become available, along with the metadata of the samples.
       
  • Publication
    • Lifeplan and the teams co-author a data paper publishing the first 2-3 years of data. 
    • Once the data paper is submitted, teams may publish their own research on their data.
    • Lifeplan and the teams co-author ecological research papers on the joint data.
Malaise trapping
  • Sample collection
    • Teams collect one 7-day sample every week
    • Teams create metadata by scanning QR codes on cyclone sampler and sample vial with Lifeplan app
    • Teams store samples until shipment, in freezer if possible
       
  • Sample shipping to Guelph
    • Teams ship samples to Centre for Biodiversity Genomics (CBG) in Guelph
    • CBG scans samples’ QR codes on arrival and shares list with Lifeplan UH
    • Lifeplan UH checks on any missing or confusing metadata with the team
    • Lifeplan UH shares samples’ metadata to CBG
    • Lifeplan UH sends copy of each team’s Material Transfer Agreement to Guelph to ensure that we have the right to process the samples, and to determine whether samples and DNA extracts will be stored, destroyed or repatriated after analysis. Malaise samples will be sequenced non-destructively, so intact individuals will remain in the sample bottles after analysis.
       
  • Sample sequencing
    • CBG performs non-destructive bulk metabarcoding of the samples
    • CBG barcodes some individual arthropods from each site, performing individual re-extraction and barcode sequencing. Number of individuals per site to be determined.
       
  • Sample imaging
    • CBG takes high-resolution bulk images of the samples, with individual insects spread out so that they are visible
    • CBG takes individual images of the individual arthropods that were barcoded
       
  • Transfer of sequencing data to LIFEPLAN
    • CBG uploads metabarcoding data to mBRAVE system to share with LIFEPLAN researchers
    • CBG sends metabarcoding data to LIFEPLAN. Includes both raw and demultiplexed + merged data as fastq.gz files, as well as UMIMap.txt files that list which file is for which sample code
    • LIFEPLAN uploads metabarcoding data to ALLAS for sharing with LIFEPLAN researchers
    • CBG uploads individual barcoding data to BOLD system, with a separate project for each LIFEPLAN team’s samples
    • Teams that want to have their raw sequencing data can request it from lifeplan@helsinki.fi. Individual sequencing data is shared via BOLD projects, with LIFEPLAN controlling access through BOLD usernames. Sample-level metabarcoding data is shared via mBRAVE, with LIFEPLAN controlling access through mBRAVE usernames.
       
  • Transfer of imaging data to LIFEPLAN
    • CBG uploads individual images to BOLD system, with a separate project for each LIFEPLAN team’s samples
    • CBG uploads shares bulk and individual images with LIFEPLAN researchers
    • LIFEPLAN uploads the image data to ALLAS to share with LIFEPLAN researchers
    • Teams that want to have their imaging data can request it from lifeplan@helsinki.fi. Individual imaging data is shared via BOLD projects, with LIFEPLAN controlling access through BOLD usernames. Bulk image data is shared via Funet filesender as it becomes available.
       
  • Bioinformatics
    • CBG performs initial bioinformatics with the mBRAVE system, where species assignments are based on matching sequences over a certain threshold.
    • Lifeplan UH/JyU/Duke performs bioinformatics with the PROTAX system, which is a probabilistic taxonomic classification software. It handles unknown taxa better than mBRAVE and gives probabilities to classifications.
       
  • Species lists
    • Lifeplan UH/JyU/Duke translates PROTAX results into species-by-sample matrices: lists of which species were found in which samples.
    • Lifeplan UH sends species lists to the teams as they become available, along with the metadata of the samples.
       
  • Publication
    • Lifeplan and the teams co-author a data paper publishing the first 2-3 years of data. 
    • Once the data paper is submitted, teams may publish their own research on their data.
    • Lifeplan and the teams co-author ecological research papers on the joint data.
Soil sampling
  • Sample collection
    • Teams collect five compound soil samples eight times a year
    • Teams create metadata by selecting their site in the mobile application and scanning the QR code on the sample bag label
    • Teams dry the samples and store them in a freezer until shipment
       
  • Sample shipping to Uppsala
    • Teams ship samples to Lifeplan SLU in Uppsala
    • Lifeplan SLU scans vials’ QR codes on arrival, and Lifeplan UH checks metadata
    • Lifeplan UH checks up on any missing or confusing metadata with the team
       
  • Sample cleaning by Lifeplan
    • LIFEPLAN SLU freeze dries the samples
    • LIFEPLAN SLU stores samples in - 20 freezer
       
  • Sample shipping to Bioname
    • LIFEPLAN SLU ships samples to Bioname in Turku, Finland
       
  • Sample sequencing
    • Bioname performs grinding and metabarcoding of the samples
       
  • Transfer of sequencing data to LIFEPLAN
    • Bioname sends sequencing data to LIFEPLAN
       
  • Bioinformatics
    • LIFEPLAN performs bioinformatics with the PROTAX system
       
  • Species lists
    • Lifeplan UH/JyU/Duke translates PROTAX results into species-by-sample matrices: lists of which species were found in which samples.
    • Lifeplan UH sends species lists to the teams as they become available, along with the metadata of the samples.
       
  • Publication
    • Lifeplan and the teams co-author a data paper publishing the first 2-3 years of data. 
    • Once the data paper is submitted, teams may publish their own research on their data.
    • Lifeplan and the teams co-author ecological research papers on the joint data.
Camera trapping
  • Sample collection
    • Teams collect five 7-day samples of images every week by collecting the memory cards from the five trail cameras.
    • Teams create metadata by scanning QR codes on the cameras and memory cards with Lifeplan app
    • Teams backup data onto external hard drives
       
  • Transfer of image data to LIFEPLAN
    • Teams upload data to Nextcloud
    • Teams connect data and metadata in the web admin
    • LIFEPLAN transfers data from Nextcloud to ALLAS
       
  • Collection of annotation data
    • LIFEPLAN selects images to annotate and uploads them to Zooniverse
    • Teams identify the animals in the images on Zooniverse
    • LIFEPLAN downloads annotation data from Zooniverse
       
  • Species identification
    • LIFEPLAN uses annotation data to train machine learning algorithm to identify animal species
    • LIFEPLAN runs machine learning algorithm on full image data
       
  • Species lists
    • LIFEPLAN UH translates results into species-by-sample matrices: lists of which species were found in which samples.
    • Lifeplan UH sends species lists to the teams as they become available, along with the metadata of the samples.
       
  • Publication
    • Lifeplan and the teams co-author a data paper publishing the first 2-3 years of data. 
    • Once the data paper is submitted, teams may publish their own research on their data.
    • Lifeplan and the teams co-author ecological research papers on the joint data.
Au­dio recording
  • Sample collection
    • Teams collect five 7-day samples of audio every week by collecting the memory cards from the five trail cameras.
    • Teams create metadata by scanning QR codes on the recorders and memory cards with Lifeplan app
    • Teams backup data onto external hard drives
       
  • Transfer of image data to LIFEPLAN
    • Teams upload data to Nextcloud
    • Teams connect data and metadata in the web admin
    • LIFEPLAN transfers data from Nextcloud to ALLAS
       
  • Collection of annotation data
    • LIFEPLAN selects sounds to annotate and uploads them to Bird Sounds Global
    • Teams and others identify the bird sounds on the recordings on Bird Sounds Global
    • LIFEPLAN downloads annotation data from Bird Sounds Global
       
  • Species identification
    • LIFEPLAN UH uses annotation data to train machine learning algorithms to identify bird species
    • LIFEPLAN UH runs machine learning algorithms on full sound data
       
  • Species lists
    • LIFEPLAN UH translates results into species-by-sample matrices: lists of which species were found in which samples.
    • Lifeplan UH sends species lists to the teams as they become available, along with the metadata of the samples.
       
  • Publication
    • Lifeplan and the teams co-author a data paper publishing the first 2-3 years of data. 
    • Once the data paper is submitted, teams may publish their own research on their data.
    • Lifeplan and the teams co-author ecological research papers on the joint data.