Completed Projects

Here is a summary of key software applications that the staff at PalaeoPi have developed over the years.


PKC

Project Title: Peakachoose

Client: NEAAR Lab, University of York

Development Date: 2010

Type: MS Excel add-in

Platform/language: Windows: VBA

Project Description: Peakachoose was developed to facilitate validation and data extraction of chiral amino acids from spreadsheets generated by a HPLC through the Agilent Chemstation software.  When activated on a worksheet saved into the root directory of a Chromatograph run, Peakachoose would find all the individual samples associated with that run and populate a list box.  The user could then choose a sample by selecting it and it’s associated chromatogram would appear in an image box.  By looking at the chromatogram, the user then decided which peak retention time represented the amino acid present in the lowest concentration.  Using this information Peakachoose would then filter out excess peaks present and produce a best guess list of amino acid peaks present.  The user then further cleaned this list by dragging junk peaks to a ‘Sin Bin’ (information used to improve peak filtering on subsequent samples).  When the user was satisfied they had only a list of the amino acids they were interested in, the user could then flag which amino acids were present and Peakachoose would use this information to grab all the relevant meta data required (usually peak area) from the relevant run files and combine them all into one sheet.

Notable Features: Installable into Excel menu, drag and drop, facilitated machine learning, and object orientated programming using classes.

Project Outcomes:  Combined validation and data extraction into one step, cutting time spent on these activities by 70%.  Reduced the rate of errors due to cutting and pasting, mislabelling etc to zero.


AMS

Project Title: The Archaeology Management System (AMS)

Client: BioArch, University of York

Development Date: 2009

Type: MS Access database

Platform/language: Windows: VBA

Project Description: The AMS was developed to reduce the admin burden of keeping track of day to day laboratory records required to keep the terms of a quality agreement with FERA.  When opening up the database the user had the ability to record new equipment coming to the lab, keep track of repairs, and calibration.  It was later expanded to include chemical safety information with the option to create/calculate and print off common reagent recipe stickers for lab books and produce risk assessments based on metadata retrieval.

Notable Features: Object orientated programming; conditional formatting; MySQL back-end; CSV and PDF file export; batch record inserting; partial string searching; time based maintenance reporting; label printing; reagent recipe calculator; user assisted risk assessment generator.

Project Outcomes:  Eliminated the need for laboratory equipment maintenance, calibration, and chemical safety records to be stored in disparate spreadsheets.   Allowed reviewers generating chemical risk assessments to see all data associated with reagents kept within the lab.


well_plate

Project Title: ZooMS (Zoology by Mass Spectrometry) manager

Client: BioArch, University of York

Development Date: 2011

Type: MS Access database

Platform/language: Windows: VBA

Project Description: ZooMS manager was developed to record peptide digest locations spotted out on to MALDI-TOF 96 and 384 well plates.  The database allowed a user to record peptide digests and their exact location on physical plates.  The user would input the lot number of the original sample that was digested into a box with a biological replicate number below.  The database then generated a unique plate number (printable as a bar-code sticker) that could be used to retrieve a list of all the samples pipetted out onto that particular plate in storage.  The bar-code could later be used to identify the plate and to also retrieve all of the metadata  associated with that plate.  In addition, once recorded in the database, a physical plate map could be printed if required.

Notable Features: Object orientated programming; MySQL back-end; partial string searching; label printing; metadata retrieval from other databases.

Project Outcomes: Eliminated the need for paper records, thus eliminating the risk of losing the records.  Allowed for the sharing of mass spectrometry sample information between all members of the ZooMS research group.


collider

Project Title: CollIDer & ChickenHawk

Client: BioArch, University of York

Development Date: 2012

Type: MS Excel add-ins

Platform/language: Windows: VBA

Project Description: CollIDer was first developed in order to take peak lists produced by MALDI-TOF through Brucker Flex Analysis and match them to a library of peptide profiles already on file that were associated with mammalian species, facilitating species identification though “finger printing” and also giving an indication of preservation status of the orignal sample.  ChickenHawk was essentially the same program but simply used a different database for a lookup table and used egg shell peptide profiles instead.  Both allowed the user in excel to import their data and produce a simple species match report with a likelihood score based upon a database of samples already analysed and peptide data retrieved from NCBI.

Notable Features: Installable into Excel menu, import and export of .CSV and .TXT files, matching of peptide masses to a library of collagen and egg shell peptide profiles.

Project Outcomes: Allowed for automatic identification of peptide masses with regards to species and rank results, this significantly decreased the time needed to extract this information from sheets by hand.  Two publications resulted from eggshell peptide identification in this way:

  • Stewart et al 2014: Walking on Eggshells: A Study of Egg Use in Anglo-Scandinavian York Based on Eggshell Identification Using ZooMS
  • Stewart et al 2013: ZooMS: Making eggshell visible in the archaeological record