2.7. Download data
To download data acquired in indiividual embryos the user activates the Data from individual
embryos link. The link takes to a submenu page, from which two options either to retrieve or
browse data can be selected. Two possibilities to retrieve data are provided either by entering an
embryo name or selecting data by metadata information.
If the Search data by parameters option is selected, the user is prompted to fill in a form by entering
gene name, cleavage cycle and temporal class (Fig. 2.7.1) Click on the Search button generates
another form, which lists the selected embryos and contains menus to specify data type, mode of
data sorting (by embryo name or data type), output file formats (ASCII, XML, or HTML for data
and JPEG, GIF, TIFF or BMP for images), as well as a window to type an e-mail address for
confirmation of the download completion(Fig. 2.7.2). An important feature of download design is
that quantitative gene expression data are downloaded by default, and, if other types of data are
additionally required, they should be selected from the Data type menu list.
Figure 2.7.1. Search form to select embryos for download.
Figure 2.7.2. Data types download form.
On selection of embryos, data types and other information the user presses the Download data
button. This shows another window, which notifies about the download start, dynamically dispays
elapsed time and contains a link to the Download result page (Fig. 2.7.3).
Figure 2.7.3. The notification about download start.
This page dynamically displays time spent on download and provides a link to the resultant tar.gz
file (Fig. 2.7.4).
Figure 2.7.4. Download result page.
This archive contains the Images directory, which stores downloaded images in specified format,
and one or several directories for data depending on the selected number of output data formats.
The data directories are named txt, html and xml according to format of downloaded data. Each of
data directories contains an embryo_list.* file, which lists the selected embryos together with
temporal information and names of scanned genes (Fig. 2.7.5), as well as the byEmbryos or
byDataTypes directory or both depending on the selected data sorting option. Each file of the
byEmbryos directory corresponds to one embryo and contains all downloaded data types listed
sequentially (Fig. 2.7.6). Each file of the byDataTypes directory corresponds to one data type and
contains data for all the selected embryos presented in sequence (Fig. 2.7.7).
Figure 2.7.5. The embryo_list.html file lists embryos.
Figure 2.7.6. Quantitative data sorted by embryo name and downloaded in html format.
Figure 2.7.7. Quantitative data sorted by data type and downloaded in html format.
If the Download data from individual embryos by embryo name option is activated, the user is
prompted to fill in the embryo name and click the Search button. This takes to another form, which
presents the selected embryo and contains menus to specify data types, mode of data sorting, output
file formats (ASCII, XML, or HTML for data and JPEG, GIF, TIFF or BMP for images), as well as
a window to type an e-mail address for confirmation of the completion of download (Fig. 2.7.8).
An important feature of download design is that quantitative gene expression data are downloaded
by default, and, if other types of data are additionally required, they should be selected from the
data type menu list.
Figure 2.7.8. Data types download form.
On selection of data types and other information the user presses the Download data button. This
shows another window, which notifies about the download start, dynamically dispays elapsed time
and contains a link to the Download result page (Fig. 2.7.3). This page notifies about time spent
on download and provides a link to the resultant tar.gz file (Fig. 2.7.4). The archive contains the
Images directory, which stores downloaded images in specified format, and one or several
directories for data depending on the selected number of output data formats. The data directories
are named txt, html and xml according to format of downloaded data. Each of data directories
contains an embryo_list.* file, which lists the selected embryo together with temporal information
and names of scanned genes (Fig. 2.7.5), as well as the byEmbryos or byDataTypes directory or
both depending on the selected data sorting option. The byEmbryos directory contains one file,
which is named after the embryo name and contains all downloaded data types listed sequentially
(Fig. 2.7.6). Each file of the byDataTypes directory corresponds to one data type and contains data
for the selected embryo (Fig. 2.7.7).
If the Browse data options are selected the user is presented with a possibility either to download
information preselected by developmental time or by group of scanned genes. Selection of any of
these options takes to a list, from which embryos of a given developmental time or belonging to a
given group of scanned genes can be selected (Fig. 2.7.9) .
Figure 2.7.9. Download data from individual embryos preselected by developmental time.
Activating an html link takes to another form, which lists the embryos and contains menus to
specify data types, mode of data sorting, output file formats (ASCII, XML, or HTML for data and
JPEG, GIF, TIFF or BMP for images), as well as a window to type an e-mail address for
confirmation of the download completion (Fig. 2.7.2). On selection of embryos, data types and
other information the user presses the Download data button. This shows another window, which
notifies about the download start, dynamically dispays elapsed time and contains a link to the
Download result page (Fig. 2.7.3). This page notifies about time spent on download and provides a
link to the resultant tar.gz file (Fig. 2.7.4). This archive contains the Images directory, which stores
downloaded images in specified format, and one or several directories for data depending on the
selected number of output data formats. The data directories are named txt, html and xml according
to the format of downloaded data. Each of data directories contain an embryo_list.* file, which
lists the selected embryos together with temporal information and the names of scanned genes (Fig.
2.7.5), as well as the byEmbryos or byDataTypes directory or both depending on the selected data
sorting option. Each file of the byEmbryos directory corresponds to one embryo and contains all
downloaded data types listed sequentially (Fig. 2.7.6). Each file of the byDataTypes directory
corresponds to one data type and contains data for all the selected embryos presented in sequence
(Fig. 2.7.7).
To download integrated data the user activates the Integrated data link. The link takes to a submenu
page which provides the number of choices for data download (Fig. 2.7.10).
Figure 2.7.10. Submenu page for download of integrated data.
If the Search data option is activated, the user is prompted to fill in a form by entering gene name,
cleavage cycle, temporal class, method of data processing and mode of information listing (Fig.
2.7.11).
Figure 2.7.11. Form used to select integrated datasets.
Click on the Search button generates another form, which lists the selected integrated datasets and
contains menus to specify mode of data sorting and output file formats (ASCII, XML or HTML ),
as well as a window to type an e-mail address for confirmation of the download completion (Fig.
2.7.12).
Figure 2.7.12. Download integrated data form.
On selection of datasets and other information the user presses the Download data button. This
shows another window, which notifies about the download start, dynamically dispays elapsed time
and contains a link to the Download result page (Fig. 2.7.3). This page notifies about time spent
on download and provides a link to the resultant tar.gz file (Fig. 2.7.4). Depending on the selected
number of output data formats this archive contains one or several data directories named txt, html
and xml according to format of downloaded data. Each of data directories contains an idata_list.*
file, which lists gene name, confocal microscope channel, temporal information and processing
method for each downloaded dataset (Fig. 2.7.13), , as well as the byGenes or byMethods
directory or both depending on the selected data sorting option (by gene or processing method or
both). Each file of the byGenes directory corresponds to one gene and contains all downloaded
integrated datasets listed sequentially. Each file of the byMethods directory corresponds to one
processing method and contains datasets for all the selected genes presented in sequence.
Figure 2.7.13. The contents if idata_list.html file.
If the Browse data options are selected the user is presented with a possibility to download datasets
preselected by developmental time, processing method or gene name. Selection of any of these
options takes to a list, from which integrated datasets of a given developmental time, on a given
gene expression, or obtained by a given processing method can be selected. Activating an html link
generates another form, which lists the selected integrated datasets and contains menus to specify
mode of data sorting and output file formats (ASCII, XML or HTML ), as well as a window to type
an e-mail address for confirmation of the download completion (Fig. 2.7.11). On selection of
datasets and other information the user presses the Download data button. This shows another
window, which notifies about the download start, dynamically dispays elapsed time and contains a
link to the Download result page (Fig. 2.7.3). This page notifies about time spent on download and
provides a link to the resultant tar.gz file (Fig. 2.7.4). Depending on the selected number of output
data formats this archive contains one or several data directories named txt, html and xml according
to format of downloaded data. Each of data directories contains an idata_list.* file, which lists
gene name, confocal microscope channel, temporal information and processing method for each
downloaded dataset (Fig. 2.7.12),
as well as the byGenes or byMethods directory or both
depending on the selected data sorting option (by gene or processing method or both). Each file of
the byGenes directory corresponds to one gene and contains all downloaded integrated datasets
listed sequentially. Each file of the byMethods directory corresponds to one processing method and
contains datasets for all the selected genes presented in sequence.