Exaltum

We base our R&D and services around standard and custom expert solutions in analyzing life science data, including and not limited to next-generation sequencing: whole genome sequencing and assembly; transcriptome and ChIP-Seq quantitative analysis; chromatin structure mapping.
Our expert knowledge of advanced statistics, data mining, machine learning and visualization methods enable us to infer knowledge and generate predictive models based on any experimental data collected, and present them in the most comprehensible format to our clients. We work with our clients from the initial stages of experiment design in order to maximize the amount of knowledge generated while minimizing the experiment funds.

Cost Structure for Bioinformatic services

Whole genome assembly - de novo

Includes:
Experiment design consultation;Identification and genotyping of SNPs; Identification of short insertions and deletions; Classification based on features such as coding, non-coding, splice sites.

Price . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 270$ per assembly
Estimated time to completion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-3 weeks

Reference genome assembly

Includes:
Experiment design consultation;Identification and genotyping of SNPs; Identification of short insertions and deletions; Classification based on features such as coding, non-coding, splice sites.
Note:
Only species with reference genomes at Ensembl or NCBI are supported.

Price . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 270$ per assembly
Estimated time to completion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-3 weeks

RNA-Seq analysis

Includes:
Experiment design consultation; Alignment to a reference with mapping statistics; Peaking calling;Gene assignment and peak annotation;Data clustering and visualization; SNP discovery;

Price . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100$ per analysis
Estimated time to completion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Defined upon agreement

ChIP-Seq analysis

Includes:
Experiment design consultation; Alignment to a reference with mapping statistics; Peaking calling;Gene assignment and peak annotation;Data clustering and visualization; SNP discovery;

Price . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170$ per analysis
Estimated time to completion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Defined upon agreement

Chromatin structure mapping

Includes:

Price . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Upon request
Estimated time to completion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Project oriented

Custom designed bioinformatic pipelines

Includes:
Consultation regarding pipeline design and tools used; Pipeline implementation (Perl/C++); Written project report with detailed description of the pipeline, publication-ready graphics, and references;

Price . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80$/hour
Estimated time to completion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-3 weeks on average

Custom designed software solutions

Programming languages:
Perl, C++, C, HTML, R
Includes:
Source code; Binaries (if applicable); Setup and installation;
Written report with a user manual and Doxygen-like documentation;

Price . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85$/hour
Estimated time to completion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Defined upon agreement

Custom designed databases

Relational databases:
MySQL, SQLite
Includes:
Database deployment on a local server; SQL scripts; Documentation which includes a general description of the database structure.

Price . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75$/hour
Estimated time to completion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Defined upon agreement

With the advent of next generation sequencing technologies, it is possible to generate tens of millions of short sequences (reads), each spanning from as low as twenty five to several hundred nucleotides in length. These technologies provided basis for a large repertoire of gnomic and genetic studies including a variety of re-sequencing projects, identification and genotyping of SNPs, discovery of variation, ect. most starting with whole genome assemblies.

Our services include:
Experiment design consultation;Identification and genotyping of SNPs; Identification of short insertions and deletions; Classification based on features such as coding, non-coding, splice sites.

Price . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 270$ per assembly
Estimated time to completion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-3 weeks

Note: Price might be adjusted with the increasing sample size

Life sciences have become an increasingly quantitative discipline. Research in life sciences rely on high-throughput methods for collecting genetic information, collectively named the next-generation sequencing. These methods generate vast quantities of genomic data and require a specific set of skills to analyze and interpret them.

Through our NGS data analysis service we provide costumers with:

a) Consulting in the initial stages of experimental design for NGS;
b) Reference mapping;
c) Visualization of genomic tracks;
d) Expression quantification and analysis;
e) Variant detection

Price . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150$ per hour
Estimated time to completion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-3 weeks

Price . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130$ per hour
Estimated time to completion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4 weeks

ChIP-Seq method combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. The approach is usually associated to map global binding sites for a protein of interest such as in case of differential gene expression.

Our services include:
Experiment design consultation; Alignment to a reference with mapping statistics; Peaking calling;Gene assignment and peak annotation;Data clustering and visualization; SNP discovery;

Price . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170$ per sample
Estimated time to completion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Defined upon agreement

Understanding transcriptome became an essential part of genomic research, a backbone for interpreting genome function, understanding development and leading research involving diseases. RNA seq refers to the use of high-throughput sequencing technologies to sequence cDNA in order to aquire information about a sample’s RNA content.

Our RNA-seq data analysis service includes:
Experiment design consultation; Alignment to a reference with mapping statistics; Peaking calling;Gene assignment and peak annotation;Data clustering and visualization; SNP discovery;

Price . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100$ per analysis
Estimated time to completion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Defined upon agreement

In the age of information, statistics has become a rising star. Large datasets and complex data structures often turn out to be a stepping stone in many government, academic and industry related areas such as medicine, psychology, education, sociology, engineering, physics and biology. We have a long-term experience in various statistical data analyses, and we are able to utilize our services starting with the experimental design followed by proposing the most adequate data collection strategies, summarizing the information to aid in its understanding, drawing conclusions and finally estimating present and/or predict future patterns. Our statistical data analysis framework is divided in three basic packages, however upon request our services can be extended to meet specific requirements posed by our clients.

Cost Structure for Statistical Analysis

Basic I:

Tests:
t-test, Chi-square test, Non-Parametric Statistics
Data:
More than 5 data points per sample, Clean Data,
Up to 5 variables

Price . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90$/hour
Estimated time to completion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8h

Basic II:

Tests:
t-test, Chi-square test, Non-Parametric Statistics
ANOVA, Regression & Correlation analysis
Data:
More than 5 data points per sample, Data Processing,
Up to 15 variables

Price . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80$/hour
Estimated time to completion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30h

Intermediate:

Tests:
t-test, Chi-square test, Non-Parametric Statistics
ANOVA, Complicated ANOVA, Regression & Correlation analysis
PCA, MCA, Extensive modeling, Diagnostic analysis ( Sensitivity,
Specificity, Accuracy, Precision, Positive Predictive Value ), etc.
Data:
More than 5 data points per sample, Data Processing,
More than 15 variables,

Written report
(for research projects)

Price . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70$/hour
Estimated time to completion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60h

Advance:

Project oriented

Price . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Upon request
Estimated time to completion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Project oriented

Scientific activities are increasingly subject to various quality assessment exercises and performance evaluations, based around the peer-review system and complemented with biblio- and scientometrics activities. With our state of the art publication analysis and visualization, we are able to calculate and present a versatile quantitative landscape of scientific activities, ranging from single research groups to the national level evaluations. As an example of our activities please refere to Croatian Scientific Landscape project available at:

http://sci.bioinfo.hr/

In fact, why limit our domain to scientific evaluations? Combining knowledge inference and data mining, we are able to tackle any ‘big data’ task thrown in our direction and generate high quality intelligence with an appealing visual interactivity!

Our expert knowledge of advanced statistics, data mining, machine learning and visualization methods enable us to infer knowledge and generate predictive models based on any experimental data collected, and present them in the most comprehensible format to our clients.

Our services include:
Data formating; Time series modeling & forecasting; Data decomposition for better pattern recognition;
ARIMA modeling; Linear and Non-linear models; Genetic algorithm optimization, PCA based modeling; Neural networks; Data visualization

Price . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100$/hour
Estimated time to completion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Defined upon agreement

Our expert knowledge of advanced statistics, machine learning and visualization methods enable us to
computational process and discover patterns in large data sets utilizing artificial intelligence, machine learning, statistics in order to process is to extract information from a given data set and transform it into an understandable and intuitive structure for easy use

Our services include:
Database mining; Literature mining; Database creation; Integration of publicly available data with data provided by a client; Data visualization

Price . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90$/hour
Estimated time to completion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Defined upon agreement

Data Analysis Services