Geena
Build June 18, 2019.
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Welcome to GeenaR, a tool for MALDI/ToF MS spectra analysis.

Using GeenaR for analysing MALDI spectra should be straightforward.
This page may help you in running GeenaR with the example files provided for testing purposes.
See also the help page and the page with information on file formats.


Introduction

In order to support the execution of a test run, we provide an example dataset and a related example target file.
The dataset is pre-loaded on the server in an appropriate folder and you don't need to download and/or upload it again.
On the contrary, the target file must be downloaded to your machine and uploade when you want to run the test.
Here below you may find a description of the files and a step-by-step guide for launching the test.
Note! This step-by-step guide only applies to the example dataset! See the help page for information on how to run GeenaR with your own data.

Files

A dataset including spectra from a study on colorectal cancer
The dataset includes 40 spectra from 10 samples (each sample is represented by four technical replicates). Six samples refer to sera from patients affected by colorectal cancer (various grade and stage), and the remaining four samples refer to sera from healthy volunteers.
You may download the dataset from here.

Here is a summary of the spectra with information on the originating sample.
SpectrumFile nameSampleReplica numberStatus
13S13569_A_SP13S13569_A_SP.txt13S135691Healthy volunteer
13S13569_B_SP13S13569_B_SP.txt13S135692Healthy volunteer
13S13569_C_SP13S13569_C_SP.txt13S135693Healthy volunteer
13S13569_D_SP13S13569_D_SP.txt13S135694Healthy volunteer
13S14986_A_SP13S14986_A_SP.txt13S149861Healthy volunteer
13S14986_B_SP13S14986_B_SP.txt13S149862Healthy volunteer
13S14986_C_SP13S14986_C_SP.txt13S149863Healthy volunteer
13S14986_D_SP13S14986_D_SP.txt13S149864Healthy volunteer
13S15816_A_SP13S15816_A_SP.txt13S158161Healthy volunteer
13S15816_B_SP13S15816_B_SP.txt13S158162Healthy volunteer
13S15816_C_SP13S15816_C_SP.txt13S158163Healthy volunteer
13S15816_D_SP13S15816_D_SP.txt13S158164Healthy volunteer
13S15947_A_SP13S15947_A_SP.txt13S159471Healthy volunteer
13S15947_B_SP13S15947_B_SP.txt13S159472Healthy volunteer
13S15947_C_SP13S15947_C_SP.txt13S159473Healthy volunteer
13S15947_D_SP13S15947_D_SP.txt13S159474Healthy volunteer
C103_A_SPC103_A_SP.txtC1031Colorectal affected
C103_B_SPC103_B_SP.txtC1032Colorectal affected
C103_C_SPC103_C_SP.txtC1033Colorectal affected
C103_D_SPC103_D_SP.txtC1034Colorectal affected
C128_A_SPC128_A_SP.txtC1281Colorectal affected
C128_B_SPC128_B_SP.txtC1282Colorectal affected
C128_C_SPC128_C_SP.txtC1283Colorectal affected
C128_D_SPC128_D_SP.txtC1284Colorectal affected
C131_A_SPC131_A_SP.txtC1311Colorectal affected
C131_B_SPC131_B_SP.txtC1312Colorectal affected
C131_C_SPC131_C_SP.txtC1313Colorectal affected
C131_D_SPC131_D_SP.txtC1314Colorectal affected
C132_A_SPC132_A_SP.txtC1321Colorectal affected
C132_B_SPC132_B_SP.txtC1322Colorectal affected
C132_C_SPC132_C_SP.txtC1323Colorectal affected
C132_D_SPC132_D_SP.txtC1324Colorectal affected
C133_A_SPC133_A_SP.txtC1331Colorectal affected
C133_B_SPC133_B_SP.txtC1332Colorectal affected
C133_C_SPC133_C_SP.txtC1333Colorectal affected
C133_D_SPC133_D_SP.txtC1334Colorectal affected
C135_A_SPC135_A_SP.txtC1351Colorectal affected
C135_B_SPC135_B_SP.txtC1352Colorectal affected
C135_C_SPC135_C_SP.txtC1353Colorectal affected
C135_D_SPC135_D_SP.txtC1354Colorectal affected
  A target file
The target file includes a list of the spectra in the dataset with related information on sample, replica number and status, appropriately formatted.

Here is the target file:
13S13569_A_SP.txt	13S13569	1	N
13S13569_B_SP.txt	13S13569	2	N
13S13569_C_SP.txt	13S13569	3	N
13S13569_D_SP.txt	13S13569	4	N
13S14986_A_SP.txt	13S14986	1	N
13S14986_B_SP.txt	13S14986	2	N
13S14986_C_SP.txt	13S14986	3	N
13S14986_D_SP.txt	13S14986	4	N
13S15816_A_SP.txt	13S15816	1	N
13S15816_B_SP.txt	13S15816	2	N
13S15816_C_SP.txt	13S15816	3	N
13S15816_D_SP.txt	13S15816	4	N
13S15947_A_SP.txt	13S15947	1	N
13S15947_B_SP.txt	13S15947	2	N
13S15947_C_SP.txt	13S15947	3	N
13S15947_D_SP.txt	13S15947	4	N
C103_A_SP.txt	C103	1	D
C103_B_SP.txt	C103	2	D
C103_C_SP.txt	C103	3	D
C103_D_SP.txt	C103	4	D
C128_A_SP.txt	C128	1	D
C128_B_SP.txt	C128	2	D
C128_C_SP.txt	C128	3	D
C128_D_SP.txt	C128	4	D
C131_A_SP.txt	C131	1	D
C131_B_SP.txt	C131	2	D
C131_C_SP.txt	C131	3	D
C131_D_SP.txt	C131	4	D
C132_A_SP.txt	C132	1	D
C132_B_SP.txt	C132	2	D
C132_C_SP.txt	C132	3	D
C132_D_SP.txt	C132	4	D
C133_A_SP.txt	C133	1	D
C133_B_SP.txt	C133	2	D
C133_C_SP.txt	C133	3	D
C133_D_SP.txt	C133	4	D
C135_A_SP.txt	C135	1	D
C135_B_SP.txt	C135	2	D
C135_C_SP.txt	C135	3	D
C135_D_SP.txt	C135	4	D

Running the test

In order to run the test, you must execute the following steps in the the GeenaR home page.

  1. Download the target file
    The target file is available at http://proteomics.hsanmartino.it/geenar/uploads/testTargetFile.txt.
    You don't need to download and/or upload the dataset, it is already pre-loaded on the server in an appropriate folder.

  2. Fill in the 'Job information section' in the GeenaR home page
    • You must specify 'example' as dataset name.
    • You should include your email address.
    • You can specify any job name or leave the suggested name.
    • You can specify your country or leave the field empty.
    For your convenience, we report here a copy of the 'Job information section'. Fields marked by a * are mandatory.
     Job information
    *Job name: You can specify any job name or leave the suggested name
    *Data set name: You must specify 'example' as dataset name
    *Email: You should include your email address
    Country: You can specify your country or leave the field empty


  3. Fill in the 'Input data section' in the GeenaR home page
    • You must select the test target file that you have downloaded for the 'Target file' field.
    • You can specify any allowed value for the fields 'Trimming From', 'Trimming To', Quality conitrol', 'Reporting', and 'With code' or leave them unchanged.
    • You should leave unspecified the 'Attribute file' (for semplicity sake).
    For your convenience, we report here a copy of the 'Input data section'. Fields marked by a * are mandatory.

     Input data
    *Target file: You must select the test target file that you have downloaded.
    Trimming: From: m/z You can specify any allowed value or leave this field unchanged.
      To: m/z You can specify any allowed value or leave this field unchanged.
    Quality control:           Reporting: With code: You can specify any allowed value or leave these fields unchanged.
    Attributes file: You should leave this field unspecified (for semplicity sake).

  4. Launch the execution of GeenaR in the GeenaR home page
    Just click on the button that is located below the 'Input data' section in the GeenaR home page.
That's all. Please do not hesitate to get in touch with us for any further information or clarification.


For information, get in touch with:
Paolo Romano, Bioinformatics, IRCCS Ospedale Policlinico San Martino,
Email to Paolo.Romano@HSanMartino.it