Make2D-DB II is an
environment to create, convert, publish, interconnect and keep
up-to-date 2-DE
databases. It converts data from various formats into a relational
format. The tool offers the possibility to automatically update data
related to numerous external data resources in a highly consistent
manner. It is also possible with this tool to dynamically interconnect
several remote databases or projects to form a virtual global database
accessible
from one single entry point.
Make2D-DB II can also be
used without any local data, as a personal and a configurable Web
portal, to link simultaneously to several remote 2D resources.
Finally, this tool can be easily used to build up a 2-DE repository,
accessible by any one from the Web.
The tool
is open source and
totally free of
charge.
Make2D-DB II is
a software to create, convert,
publish, interconnect and keep up-to-date 2-DE
databases. Being open source (cf.license),
it is distributed totally free of
charge.
With
this tool, one can
easily convert any existing personal federated
2-DE database (including
databases
built with the first
make2ddb package or following the SWISS-2DPAGE
conventions) into a more reliable format. The tool also
handles XML exports
from Melanie / ImageMasterTM
2D Platinum,
common spreadsheets
(e.g. Excel
/ CSV
reports)
as well as simple text
lists.
It is also possible to create new relational databases from
scratch.
It runs on most UNIX-based operating systems (Linux, Solaris/SunOS,
IRIX).
Being
continuously developed, the tool is evolving in concert with
the current Proteomics
Standards Initiative of the Human Proteome Organization
(HUPO).
Make2D-DB
II is designed to
ensure high consistency of data.
It allows dynamic interconnection between
any number of similar remote
databases and offers many other features, including automatic data
updates related to external data, dynamic cross-references to similar
databases, intuitive
search engine and data visualization combined with exports in various
formats.
In
addition, the tool
extends the concept of 2-DE
databases to cover a more elaborate description of
proteomic experiments and analysis. Currently, it can integrate various
annotation documents (e.g. sample and gel preparation), as well as many
common analysis
file formats (e.g. common mass spectrometry formats, mzData, etc.).
References to other remote repositories can also be easily integrated
(e.g. PRIDE for MS/MS related data). Users can also
define their own types of annotations and easily integrate them within
their data representation.
Even with no local data, any laboratory can easily build up an
intuitive Web portal accessing as many remote 2-DE resources as desired.
The Web interface appearance can be personalized for everyone's taste. Data can be
marked to be public, as well as fully or partially private. An
administration Web interface, highly secured, makes external data
integration, data export, data privacy control, database publication and versions' control a very easy task to perform.
Assistance
is provided to
help users install the tool and to use its numerous features to their
best advantage. In addition to the distributed documentation files,
this site will be
continuously updated to include hints, news and frequently asked
questions.
WORLD-2DPAGE - A Dynamic Portal to query simultaneously World-Wide 2-D PAGE Databases
2DBase-Ecoli - A 2D-PAGE Database of Escherichia coli (various growing conditions) at University of Bielefeld - Fermentation Engineering Group (AGFT), Germany
Cornea-2DPAGE - Human cornea samples (at various pI ranges), Department of Molecular Biology, Faculty of Science, Aarhus University, Denmark.
DOSAC-COBS 2D-PAGE - various human samples (breast cancer, lymphocyte, mammary cells, HL60 and U937 cell lines), Departimento di Oncologia Sperimentale e Applicazioni Cliniche / Centro di Oncobiologia Sperimentale - Università degli Studi di Palermo.
KAIKO 2DDB - the Silkworm-2DPAGE (various organs, tissues at various developmental stages) from National Institute of Agrobiological Sciences, Japan
Peroxisomal-2DPAGEMus musculus Liver, SCB Group, Uppsala University, Sweden.
Plasmo2DbasePlasmodium falciparum 2-DE database at Indian Institute of Science, Bangalore, India
REPRODUCTION-2DPAGE 2D-PAGE database (Human ovary, Mouse testis) at Lab of Reproductive Medicine, Nanjing Medical University, PR. China.
ExPASy Home page
The
Make2D-DB II Package
YPRC Korea