ismeralda

Welcome to ISMeralDa ! PDF Print E-mail

ism browser screenshotISMeralDa stands for "Interdisciplinary Science Management Database". It is designed to support scientists in most of their daily operations  and make the scientific process more transparent and sustainable for all. ISMeralDa is an advanced open-source software concept for managing highly interdisciplinary scientific projects by structuring and documenting the project ideas and experimental results. It furthermore supports an easy and secure way of sharing documents with scientific colleagues, synchronizing all of the projects work. All group members will be informed about the latest project state. New colleagues will see the whole developing process of a project and can immediately start upon what was already achieved and build. ISMeralDa's user interface has many build-in tools for planing, evaluating, documenting, archiving and publishing experimental data. It tries to unify all the processes starting from planning, ordering of materials, retrieving related articles, archiving experimental results and raw data until writing a publication and discussing the results with colleagues. Even if You are using ISMeralDa as a single scientist or student, you can already benefit from the protocols, recipes and tools the ISMeralDa database is provided with.

By automatizing many routine operations and supporting to channel ideas and thoughts, it enables scientists to focus more on their very own interests and intent: exploring and finding out . Present day's science publication tradition is very much focused on "getting out" an article in a journal. Such article types usually represent a subjective interpretation of the authors. They interpret the data according to their knowledge and with the set of theories of their time. Future reinterpretation of the measured data is very difficult because the process details are often not completely described. ISMeralDa is intended to store data in the most interpretation-free (objective) form possible.

It is designed to shift the scientific paradigm from a publishing driven to a question driven science.

To maximize the interdisciplinary ISMeralDa follows an "holistic approach": most common parts of the scientific work shall be represented and supported by the software.

Enjoy developing and using ISMeralDa !

On behalf of the development team,

mark doerr

(please address any comments, questions and support to mark[at]ismeralda[dot]org


(planned) Key-features of ISMeralDa

  • planning experiments
  • organizing literature - storing references together with the PDF documents and other files
  • feature rich lab book (GLP conform)
  • managing experimental data
  • versioning system - keeps track of all changes and who changed/added what
  • sharing selected data with colleagues in a secured way
  • documenting all experiments - also negative results (to prevent a second invention of the wheel)
  • writing collaborative publications
  • strong calculation, simulation and data visualization tools included
  • expandable plug-in architecture
  • multi-platform software architecture - runs in most common computer environments (Linux, Apple OS X (R), Microsoft Windows(R))
  • open design - open source, software fully transparent and documented, for everyone available -> no black box, full control of data (would You trust a system, you are not allowed to understand ?
  • open peer reviewing model
  • distributed network file repository
  • one consistent program user interface with a balance between simplicity in usage and demand of functionality (systems complexity grows with the demand).
  • long term storage of full research data - survives changes
  • open data format that can be used for future artificial intelligent systems to interpret data
  • multilevel, open reviewing system - to prevent manipulation/fraud and increase reliability and consistency of scientific data

easy, useful, stable

Technology behind ISMeralDa

ISMeralDa is assembled using the technology of most successful open source tools like

  • mySQL/SQLlite (www.mysql.org/www.sqllite.org) as database back-end
  • QT4 front-end / GUI interface (www.trolltech.org now: nokia)
  • libpoppler () as ducument viewer / PDF annotater
  • webkit() as HTML renderer
  • git () as document versioning system

For whom is ISMeralDa made ?

For Single Scientists

  • supporting from the planning stage to assembled presentation or publication
  • organizing the literature (bibliography, article database, PDF and supplemental information)
  • keeping an inventory of the devices and material to be used
  • calculation and evaluation tools (molecular calculator, MS, HPLC, plot, statistics, ... )
  • tools for the need of common tasks (concentration of RNA/DNA, PCR, .... )

s. section for special features ...

For Students of Science

  • learn, how to design experiments, structure data
  • organize the experimental work in a professional manor
  • share your results and work together with Your colleagues

For Workgroups

For Collaboration of Work-groups

  • planning the project
  • secure sharing of current data
  • inform all group members
  • keeping a history (archive) of what was done in the past for new group members

For Scientific Institutes

  • Keeping track of their orders, chemicals, inventory - the work to upkeep the database is shared by all scientists, there is no extra personal need
  • cost reducing,
  • efficient

Companies

  • providing interface to only one software

Examples of how scientist benefit from ISMeralDa

Molecular biologists

  • calculate properties of RNA or DNA oligomers
  • planning PCR, cloning experiments
  • keeping a database of oligomers
  • storing sequence information
  • choosing the best buffer systems
  • protocols

Cell biologists

  • making a database of cell lines

Synthetic oriented scientists

  • plan their experiments
  • calculate the amount of reagents to be used
  • order chemicals and material
  • document the reactions
  • collect all the characterizations - even directly from the instrument -
  • summarize the findings in reports
  • assembling a journal article

Physicists

  • organize their projects
  • collect their raw data and results at one place

Environmental scientists

  • database with commonly micro-organisms, plants and animals

Keywords

LIMS, laboratory notebook, sequence database, bibliography, collaborative writing, organizer, molecular weight calculator, periodic table of elements, DNA calculator, RNA calculator, PNA calculator, LNA calculator, interdisciplinary, chemistry, physics, biology, structure editor, planner, laboratory notebook, mindmap

 
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