Products and services

GetDB	UVSS	Consulting

GetDB

Biologists, bioinformaticians, and scientists need to have direct access to various molecular biology databases. Their formats are heterogeneous, and automated means are needed to mine them for updates in a simplified way. Genomining has created GetDB as a solution for this specific need.

GetDB saves you time

With GetDB, public or private databases of one's choice can be subject to workflows. External databases are automatically downloaded on internal storage system. Specifications for sorting out only the updates allows to download only the novelties since the latest database download. After installing the databases, GetDB checks that the data is syntaxically valid.

In order to optimize the later use of the imported data, GetDB automatically controls :
- Automatic execution of workflows each time a database is updated
- Generic methods allow the integration of various databases,
- automated formatting of biological databases,
- Management of outdated data, - Référence version of database creation, - The restart of downloading after an incident,
- Follow-up of version, size and usage rate,

Configuration options allow the execution of specific functions (indexing, formatting, and validation) at the various download and installation steps. Tools are provided for turning existing software into plugins allowing the design of powerful workflows.

GetDB is based on well known industrial standards (Linux; PostegreSQL; Perl). Installation and maintenance are provided by Genomining.

GetDB documentation (english version) (Acrobat/PDF)

Use cases :
- Keeping human DNA array annotations updated (Acrobat/PDF)
- Genome mapping & statistical analysis of retroviral instertion sites (Acrobat/PDF)
- Keeping RefSeq non-redundant and continously updated in-house (Acrobat/PDF)
- Easy creation of a focused and automatically updated subset of RefSeq files (Acrobat/PDF)

You need to easily run large virtual-screening pipelines, you want to use different docking engines on the same platform. You need to post-process your results in a way independent of the docking tool used. You want a fault tolerant system capable of dealing with unpredictible hardware failures. You do not want erroneous ligands to crash your entire pipeline. Then UVSS will let you achieve all these requirements.

Genomining's team can avail itself of rare skills and experience in terms of both molecular biology and information technology.

This double specificity allow Genomining to offer "made to measure" services to the life science industry :
- Consulting on conception of IT solutions for high throughput data acquisition platforms
- Assistance in solving specific data collection and mining, especially repetitive and exhaustive queries regarding biological objects
- Rapid and specific developments, based on Genomining's toolbox, in view of optimizing the discovery of information in biology, and allowing to speed and rationalize the discovery of novel therapeutic targets.

Examples / experiences :

Assistance in collecting information on a protein
Assistance in supplying the bioinformatic support for a 100 person R&D unit
Creation of an intranet allowing a team of scientists to access all the information relative to therapeutic targets.
Conception and organisation of the acquisition phase in a high throughput biology production centre, or for a specific project (e.g. sequencing project, DNA chips...)
Automated annotation of whole genomes
Analysis of genomic regions to identify candidate genes (disease, trait...)
Downloading and comparison of heterogeneous data ( e.g. genetic maps, cDNA, SAGE tags, mass spec signatures...) in view of a rich annotation.
Training activities
Consulting activities

Genomining guaranties the best standards in quality and in confidentiality.