Accessing instrument data

Overview

All data collected in Teaching Labs is provided electronically, usually within a few minutes of collection. This page provides information on how to access data from various instrumentation, with files made available in multiple formats.

Instrument types

Instrumentation in the Teaching Laboratories is broadly grouped into two methods of use. There are instruments which you are able to walk up to, use, and immediately obtain your results, for example IR, and UV-Vis. There are other instrumentation which relies on data submission, where you prepare a sample for this to be added to an instrument queue which will then be recorded later (usually overnight). The approach to finding data varies depending on the method of submission, with details for each given below.

Walk up instrumentation

Instruments where data collection is generally less than a couple of minutes
Users record their own data and obtain a filename immediately
Need to record which instrument was used to acquire data
Includes IR, UV-vis and microscopy

Sample submission services

Instruments where data collection is generally longer than a couple of minutes
Users submit a sample and complete a submission form to request data collection
Will need to look up sample status and filenames in submission spreadsheets to be able to locate data
Includes NMR, HPLC, GC and scXRD

Accessing data

There are multiple methods provided to access data collected in Teaching Labs. Each route give access to the same data, but differ in their use. Webfiles is very simple to use and is good for locating and downloading individual files, whereas the SFTP service is better for downloading larger quantities of data (including folders), but is a bit more complicated to use.

All services are provided and managed by IT Services, who also provide their own guides to their use (for multiple operating systems) which are linked from the specific pages.

Webfiles

Simple web based file access
Can only download one file at a time
Available to all students and staff at the University

SFTP

Requires a SFTP client and setup
Can download data in bulk
Available to all students and staff at the University

SMB

Network drive access
Works in a similar manner to local filesystems
Available to final year project students, graduates and staff

Quick reference

Webfiles

https://webfiles.york.ac.uk/chemtl/

SFTP

sftp://sftp.york.ac.uk/shared/storage/chemtl

SMB

\\storage.its.york.ac.uk\chemistry\services\tl

Instrument directories

Finding the right location to look for data

Data is stored inside subdirectories which are organised by instrument type. Details for where to locate data for a particular instrument can be found in the relevant instrument pages. Generally it is easiest to go to the instrumentation page for the data you want to access, and copy the link provided on that page.

Instrumentation data folders

In order to access your data, you will first need to identify the folder location for the data on the Teaching Labs Data Server. Visit the appropriate Instrument Webpage for the data you are trying to access and locate the folder name in the 'Accessing Data' section. The page will also provide information on the formats available for the instrument data, and the file naming conventions used by that instrument.

Instrumentation data folders

The list below summarises the folder names and the instruments this data relates to.

AGC: Agilent 6850 GC
CE: Capel capillary electrophoresis
cv: Cyclic voltammetry
Fluorescence: Shimadzu fluorimetry
GC: ATI Unicam 610 GCs
HPLC-Agilent:
HPLC-Jasco:
IRB:
Log:
Microscope:
MS:
nanalysis:
NMR:
PEIR:
Photometer:
Raman:
Sample Data:
stopped_flow:
test:
TGC:
UVJ:
UVS:
UVShimazdu:
UVT:
XRD:

Data formats

Data is collected in a wide variety of different formats, and the provide details on the formats provided for specific instruments. In general these can be categorised as:

PDF files

Automatically produced plots of data
Provide a quick overview of results
Usually only limited data analysis is possible

Reprocessable formats

A format which can be easily imported into software for reprocessing
Usually contains metadata from the acquisition process
Allows data to be processed to make it presentable to a scientific audience

Raw data

Raw data in a text format, typically consisting of X and Y values
Can be processed, often programmatically in bulk
May lack metadata describing individual files
CSV is the most common format

Proprietary formats

Vendor specific format for a particular instrument make
Data is often only readable by the vendors software
May contain more information about the data acquisition
Usually only the PCs for these instruments can read the files

In general, in year 1 you would expect to be using the PDF files which have been automatically produced. In year 2 onwards, you would usually be expected to be reprocessing your data.

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