BioAware: BioloMICS Software

BioloMICS

BioloMICS is certainly the most complete software solution for the storage, the analysis and the publication of biological data. Virtually any types of data can be properly archived in BioloMICS databases, ranging from morphological, physiological, biochemical, chemical, chromatographical, electrophoretical, DNA, RNA or protein sequences to bibliographical, taxonomical, geographical or administrative data (and many others as well). Pictures, URLs and files of any formats can also be linked to records and easily viewed.

The strengths of BioloMICS are not only in its incredible storage capabilities. The advanced searching tools methods developed allow complex queries and selection of records. The identification module is based on similarity methods and allows polyphasic comparisons. This means that all types of data can be used and weighted for the identification. A large panel of classification and statistical methods are also available and dendrograms, phenetic, phylogenetic trees, 2D or 3D graphical reports can be produced and exported.

With the BioloMICSNet (Internet version) or the BioloMICS CDROM modules, data can be published and extremely easily made accessible for Internet users and clients. After years of developments, the current version includes so many features that it?s virtually impossible to cite all of them. A few of the available modules are shortly described below.

Create self-designed databases

BioloMICS was originally created for the biologists not having access to existing IT infrastructures nor dedicated developers. With BioloMICS they can create their own database(s) and modify them at any time without the need for any third party intervention nor prior programming or databasing skills.

The following type of fields can be included in a user-defined/created database

Continuous data, range (min, low percentile, high percentile, max)
Continuous data, single value
Discrete data, single state
Discrete data, multiple states
96 wells microplate continuous data (absorbance values)
384 wells microplate continuous data (absorbance values)
96 wells microplate discrete data (-, +, weak, ...)
384 wells microplate discrete data (-, +, weak, ...)
Free array data, continuous data
Free array data, discrete data
Molecular weights from electrophoresis analysis, e.g. RAPD, RFLP, PCR, AFLP, ?
DNA sequence data
Protein sequence data
Text, administrative field
Date field
Bibliographic information field
Taxonomic information field (ex: links to Mycobank or other taxonomic databases)
External files link including URL, pictures and others files
Latitude and longitude coordinates
...

Access to database can be restricted (read, write, delete) per user (each user has a specific login and password allowing differential access to databases) and per fields within a database. Some users can see all the fields while others can only view and use a portion of them. Database access is defined by the owner/administrator of the database.
Fields can be re-ordered, re-organized and grouped by the administrator according to their type (for example), e.g. under the group Picture, fields Macroscopic pictures, cells pictures, ascospores pictures could be found.

Managing data

Main module: many new features have been added to the main managing module since the last version of the software and listing all of them would be too long. The main functions are:

Add, modify, delete tables within a given database (restricted to the administrator of the database)
Add, modify, delete records within a table (can be restricted by the administrator to a some users). Multiple records update with the same value. Automatic appending or replace of fields? data.
Data and records can be moved/duplicated from one table to another.
Display data in an administrator designed form view or as a sheet view (Excel like).
Records can be sorted (ascending or descending) by any field.
Linking of records data with the taxonomic database at levels ranging from Kingdom, division, class, family, genus, species, subspecies, variety or form. Obtain all relevant taxonomic information (synonymy, basionym, anamorph-teleomorph connections for fungi, type strain/specimen, bibliographic information, ?) at a double click. Records are automatically updated when taxonomy/nomenclature is changing.
Automated recording of all records and fields modifications, dates of modifications and users performing them. For each record and every fields all previously stored values can be restored. This tracking option is a major security improvement over the previous version of the software.

Import & Export of data

Exportation/printing of data in text, tab delimited, html, XML, MS-Excel or MS-Word formats. Fields to be exported can be selected by the user and self designed MS-Word templates can be used to export data in ready-to-use/print documents. Bibliographic data can be exported to tab or coma delimited, RIS, Medlars or user-defined formats. Pictures can be exported phenetic or phylogenetic trees, 3D views of PcoA analyses to bitmaps or the clipboard. Sequences to Fasta. Multiple-alignments to GCG/MSF, Nexus, Clustalw, NBRF/PIR, Phylip, GDE formats.
Special exports for some specific types of data (e.g. sequences in Fasta format, pictures in bitmap, ?).
Importation of tab delimited data and clipboard (for all types of data), Fasta format, Genbank (for bibliography, sequences and associated data), Standard Chromatogram File SCF (coming soon for raw DNA sequence files or AFLP like data), BioGalaxy electrophoresis format (for electrophoresis molecular weights data) tab or coma delimited, RIS, Medlars, PubMed (for bibliographic data).

Microplate readers connection

Automated reading and import (through RS-232) of 96 wells microplate data from 5 different brands of microplate readers (Asys Digiscan 400, the Expert 96, Labsystem Multiscan, BioTek ELx800G, BioTek ELx808G and Molecular devices Emax ? also labelled Biolog Microstation). Automated transformation of data based on user-defined formula for storage in discrete data 96 wells fields.

Pictures viewer and measurements

Pictures viewer can display any electronic images stored in one of the following formats: *.bmp,*.dib.,* *.ico, *.cur, *.wmf, *.emf, *.jpg, *.gif, *.png, *.tga, *.pcx, *.pict, *.tiff. Multiple measurements of visible structures (e.g. cells, ascospores, colony diameters, ?) can also be done. Basic descriptive statistics and information (number of observations, mean, minimum, maximum, median, percentiles (e.g. 5% and 95% but can be defined by the user), standard deviation, variance, sorted data) can be be obtained and used to be stored in the relevant field. Colour retrieval and splitting in Red Green Blue RGB values can be obtained for any given point of a picture.

Measurements on pictures, click to enlarge

Geographic data

Geographic data viewer allows maps (shape files) to be displayed. Records can be plotted on those maps and exported to the clipboard. A very large database of world locations has also be compiled is provided with the BioloMICS software. It contains the exact coordinates (latitudes-longitudes) of more than 5.5 millions locations from all over the world as well as altitudes, monthly precipitations and temperatures data for more than 10000 meteorological stations all over the world. Additional features are also available but not explained here.
Geographic locator module: In order to be able to correlate taxonomic, morphological, physiological, molecular and any other types of data with climate (temperatures, rainfalls, ?), geographic (elevation, vegetation, land use, ?) it was important to know the exact origin of the strains in terms of latitude and longitude. To be able to do this, a very large and rather exhaustive database containing about 5,500,000 locations in the world with their latitude, longitude, elevation and a few additional data (when available) like population in 2000, housing units in 2000, land area (square meters), water area (square meters) has been created. Another database containing meteorological data retrieved from 10,093 WMO (World Meteorological Organization) weather stations was built. A software connected to the BioloMICS program was made to compute distances between the closest WMO stations and the isolation points of the strains. When the horizontal and the vertical (i.e. elevation) distances are smaller than 50 Km and 500 meters respectively (those values can be changed by the user), the WMO weather data are attributed to the record and are therefore further usable for correlations with other types of data. In the near future, additional ecological/environmental databases will be built to enrich our knowledge related to the strains. A map viewer (for shape files, *.shp) was also developed in order to print the location of isolation of the strains.

Bibliographic data

The bibliographic module has all the functionalities of all the major players in the field like EndNote, Reference Manager or ProCite for example. Unlike those software, it is (also) used to store all the bibliographic data linked to the records of the database in a proper way. The following fields are available: author(s), book author(s), editors, title, journal, publisher, volume, issue, page(s), year, keyword(s), remarks, abstract, URL, ISSN, ISBN. For some of those fields, the text can be formatted (italics, bold, font size, ?). Data can be imported from and exported to the following formats: tab or coma delimited, RIS, Medlars, PubMed and users-defined formats. Basic and advanced queries can be performed on the local database and at the same time on the PubMed database. When references are available on PubMed but are not on the local one, they can be imported by a simple click.
The taxonomic database was created to store important taxonomic data related to the following levels: kingdom, division, class, family, genus, species, subspecies, variety and form. Fields available are: status of the name (current synonym, uncertain, ?), basionym of the name, type information, type strain #, remarks, last modification date, morphic state of species (anamorph, teleomorph; for fungi only), full classification, obligate synonym(s) and taxonomic synonym(s). The coding of the data is done using a wizard that was made to limit coding mistakes. When updates or modifications are made to the taxonomic database, all the records of the main database related to those updates or modifications are also automatically updated or modified. A tree-like representation of the hierarchical relations between the records is provided. This allows a user-friendly and a global viewing of the data points and their relations. A basic searching tool is also associated with taxonomic database. The whole database can be exported as text or XML file.

DNA & protein sequences

Both types of sequences can be aligned in 3 different ways:

Single sequences pairwise alignments: 2 sequences can be aligned using 6 different alignment algorithms, Fasta, Fatsa reversed, Ssearch 3, Ssearch 3 reversed, Opt2Dir and Pes2Dir (2 bi-directional alignment algorithms especially designed for this new version of BioloMICS).
- Pairwise alignments against large and externally stored sequences databases using Blastn, Fasta or Ssearch 3
- Multiple alignments using the Clustalw software. Further editing of the aligned sequences can be performed using BioEdit or GeneDoc (freely available on the Internet). Multiple alignments can be exported to a series of formats (GCG/MSF, Nexus, Clustalw, NBRF/PIR, Phylip, GDE) and further analysed by Paup* 4.0 (must be obtained separately) through a list of commands that are directly accessible from the BioloMICS software. Distance matrices based on the multiple alignments can be exported to text files and trees based on one of the available agglomerative clustering methods can be produced.
The Protein and ORF finder module allows an easy finding of ORFs and protein sequences based on DNA sequences. Resulting protein sequences can be exported to the clipboard.
Searching for sub-string and restrictions sites in sequences database is possible.
Sequences can be imported and directly linked to records of the database using the ?Sequences manager? module. Based on users-defined queries like ?Fungi[ORGN] AND 200:10000[SLEN] AND 2003/06/16:2003/07/15[MDAT]? (this a simple example but more advanced queries can also be performed) where all sequences of fungi with a length ranging from 200 bp and 10000 bp modified during the period between the 16^th of June and the 15^th of July 2003 will be downloaded and linked to the records of the currently opened database. The linking with the database can be done using a series of keywords. When a sequence based on a given strain (e.g. CBS 14) is downloaded, the software is searching the field where the strain numbers are stored and if there is a match (i.e. if the record found is the one of strain CBS 14 then the software will search, again on the basis of keywords defined by the user, the field(s) that are matching the description of the sequence. When this double match (matching the strain/record and the type of sequence/field) is OK, the sequence is stored in the database. At that time all additional data attached to the downloaded sequence can also be store in other fields like bibliography (once again on the basis of keywords defined by the user). This system allows a rapid and very efficient download of very large amounts of sequences and sequences related data to the database. Another option of this module is the automated sequences retrieval based on species names. With this option the software is screening the database and searching GenBank for matching sequences. When found, sequences are downloaded and linked to the matching records and fields. After the importation, a report is produced to inform the user/owner of the database which records were appended with the new downloaded data.

Electrophoresis

See BioGalaxy for more information about the available features. BioGalaxy is now fully integrated within BioloMICS.

Compilation of records

Using the ?Compilation of data module?, records can be selectively compiled into one record containing all the values of the original one. This option can be used, for example, to automatically create species descriptions on the basis of a selection of strains/specimens.

Growth curves

The ?growths curves? module allows the automated reading of microplates at user-defined intervals (minimum 30 seconds) and repetitions. Up to 96 growths curves are produced automatically and the original raw absorbance values as well as the graphs can be exported to the clipboard.

Clients, orders and storage manager

Client manager where all data related to clients of BioloMICS databases can be archived and used to ordering
Storage manager allowing easy placement and retrieval of stored items. Exact positions, quantity, pricing and many more data can be included in the Stock database. Items can then be searched and selected for the automated creation of orders/invoices.
Orders manager allows the linking between items to be sold, the clients and the stock databases. All orders are archived and follow up of invoices can easily be done

Query databases

Easy to use advanced searching tool, allow to query any type of field using the best possible method. For example a field containing size data like from 5-10 could be searching in up to 5 different ways while DNA sequences can be aligned using 4 others algorithms (such as Blastn-like algorithm for example). This major functionality allows users to select records with a given set of properties or to identify an unknown organism at the species level (for example). Advanced/complex queries containing questions separated by AND, OR, NOT and using brackets for their grouping can be performed.

Polyphasic identification & classification

Identification and classification module: a proper storage of data allows using them in the best possible way. The new version of BioloMICS has a newly designed algorithmic core module with many new algorithms that have been designed to be extremely fast, parametrical and flexible.
The identification option allows selecting any combination of any records from any table to be compared with any other or identical combination of records on the basis of a selected set of fields. For each fields a different algorithm (among a list of one to 6 depending on the type of field/character), weight (ranging from 0 to 100 with steps of 0.01) or tolerance factor (for fuzzy logic comparisons) can be used. It means that polyphasic (using any combination of types of characters like morphological, physiological and molecular one, for example) identifications can easily be done. Identification reports show the best hits to the unknown. Records are order by decreasing similarity (other sorting methods are also possible) and pairwise comparisons for all fields can be displayed using a series of specialized viewers for the different types of fields/characters.
After the selection of the records to classified, the classification module allows the grouping using 4 different types of methods:
- Agglomerative clustering : agglomeration of objects/records starts with the most closely related pairs of objects and gradually links to less closely related objects. When objects are associated in one cluster, no further dislocation is possible. Reports are displayed in the widely used and appreciated graphical tree-like representation. Several agglomerative clustering algorithms are available: UPGMA, UPGMC, WPGMA, WPGMC, Single Linkage, Complete Linkage, Neighbor Joining, Ward or Lance & Williams Flexible Clustering. The most commonly used are the Unweighted Pairgroup Method using Arithmetic mean (UPGMA), the Weighted Pairgroup Method using Arithmetic mean (WPGMA), the complete-linkage and the single-linkage methods. These methods differ in the way the distances are calculated when new members of a growing cluster are included. In single linkage, when an object or a group of objects i are to be linked with another cluster j, the smallest distance between a member of group i and a member of group j, is the distance at which both groups are connected. In complete linkage, it is the distance between the most distant members of both groups and in UPGMA it is the average distances between all members of both groups. In UPGMA, no weighting related to the relative size of the groups to be joined is performed, contrarily to WPGMA. Neighbor-Joining (NJ) is another agglomerative-clustering method aimed at the construction of phylogenetic trees. The NJ method tries to find the shortest possible tree. It is usually used as an alternative to parsimony methods, which can be slow and computationally intensive.
- Divisive clustering: all objects/records initially belong to the same single cluster, which is gradually broken down into smaller clusters. The division process is stopped when an a priori decided number of groups is obtained (note: other methods of stopping can be applied). Groupings are never definitive and objects can be clustered together at a certain level, then be separated and (possibly) later re-grouped again with some members of the original group. Results are displayed as lists of records belonging to the different groups with distances intra- and inter-groups.
- Principal coordinate analysis (PcoA): PCoA is a member of a larger family of techniques, called ordination methods, that include Principal Component Analysis (PCA), Seriation, Multidimensional Scaling and Factorial Analysis as well. In PCoA the space is reduced to fewer dimensions, usually 2 or 3. In fact, PCoA is just a rotation in a multi-dimensional space of the original system of axes. The original axes, representing the characters/fields of the objects/records, are replaced by new orthogonal axes, which carry most of the variance. Two or three-dimensional graphical representations can be proposed. PCA and PCoA are usually superior to agglomerative-clustering methods in the global representation or positioning of groups of objects. However, these ordination algorithms are less efficient in the representation of closely related objects.
- Functional analysis: is a method allowing the grouping of objects/records and of their characters/fields at the same time using agglomerative clustering methods. Objects are compared with one another on the basis of a selection of characters. The obtained distance matrix is latter represented as a phenotypic tree using one of the selected agglomerative clustering methods. The characters are first normalized and reduced (note that some DNA or protein sequences can not be used as such in this method), then correlated with one another to obtain a correlation matrix that can be displayed in a tree-like representation using on of the available agglomerative clustering methods available. The result is finally displayed as a double tree. The first is vertical showing the relationships between the objects/records. The second tree is horizontal and shows the groups of characters/fields that are positively (or negatively, depending on the display method used ? ?positive? or ?negative? clustering) correlated. Between the two trees a coloured table show the states of the characters/fields for the different objects/records. With this method, it is easier to isolate characters or groups of characters that are associated with some groups of objects.
- In the near future, analyses of large amounts of data combining the advantages of those different methods will be developed. Users will be able to use PcoA, divisive and agglomerative clustering methods in a serial manner.
Distance matrices of identical sizes and based on the same objects/records but on different sets of characters/fields can be combined or merged and further analyzed by PCoA or agglomerative clustering. This also allows the re-use of data obtained from third parties or from previous analyses. Correlations and distances between those different matrices can be computed and can be stored in ?characters set? matrix allowing the production of ?super trees?. The latter shows how similar are the classifications obtained by the different sets of characters.

Publish data via CDROM

The ?CDROM creation module? is made as a wizard for the automated creation of CDROM containing a selection or all the data of the main database. The CDROM software and related databases can then be packed in a package that is freely (or not; depending on the policy of the owner of the database) distributed or downloadable from a website.

Publish data on the Internet

The ?Website database creation? module is based on a wizard. After exportation, data can be published on the Internet using the BioloMICS Web software. Owners/administrator of databases, do not have to export their data to static html pages or to create additional Internet based software for publishing their data. This feature is a major breakthrough of this new version of BioloMICS. Click me for some websites based on the BioloMICS Net version. The BioloMICS Net version is not intended to replace or to be a light substitute of the main version. It is only intended for the publication of databases prepared with the main version of the BioloMICS software.

Hardware Requirements:

The BioloMICS software is compatible with all MS-Windows operating systems (95, 98, Me, NT 4.+, 2000, XP). It will work fine on Pentium II or more with 64MB RAM. Higher values would however be better. A very good graphic card is needed.

Current Main BioloMICS Version #: 7.5.88

Current Internet BioloMICS Net Version #: 4.1.0

Demo Movie: Click Here

Request Online Demo from us: Click Here

To do it, you will need a Skype account and associated software (this is free for download at Skype). You can then contact us via Skype. Click here to do it now. The demo will be done via the GoToMeeting software (a remote desktop application that you do NOT need to download nor buy). When the date and time of the meeting will be established, we'll invite you for a free tour of the software. We'll be able to answer all your questions, live !

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