Database Development - Science topic

My favorite is OpenBioMaps :D which was designed to create an manage biodiversity related databases...

Dear Srdjan Atanasijevic,

Yes. You pointed to the important conditions for the development of big data analysis technology with the use of Big Data Analytics.

Thank you, Regards,

Dariusz Prokopowicz

many databases available to manage and organize the databases. you can visit github.com repository

Informative question

Safeguarding Big Data Systems against possible intrusive information sabotage is , at least to me, the most significant requirement. In other words, security and confidentiality are top priority requirements.

I am with Alexander & James on this. First, Nearly, all so-called big-data is "it-is-what-it-is" data (i.e. The analyst has no control over how the data is collected. Under these circumstances the selection process for the sample is non-random & the selection probabilities are typically unknowable. One is often not even certain if the sample is from 1 unique population.) Under such circumstances biases can arise & their effects are not measurable. For something like sales; big-data can be highly applicable & population specific because it represents a sample from one's particular population: your customers. Yet, if it represents health records, one has to wonder whether or not the source for these record misses some parts of the population or over-represents sub-populations. I think solid "statistical thinking" can help big-data analysis more than the other way around.

your Question was not clear enough so you could get help

However, I recommend you this publication of mine you might find usefull

Thank you Dr. Robert, Dr. Ahmed and Dr. Brunno for the information.

Dear Muhammed,

I always use the '2+4 rule' for my primer design.

The '2+4 rule' is a rule of thumb or empirical formula, but it works very well in the practice.

The other formulas are theoretical approaches.

Try to use standard primer (10 A/T and 10 G/C). 

G/C rich primer are often unspecific.

Best regards,

Thomas

I must disagree sorry, but Physionet is not always a reliable database according to my short experience. For all I know, take a random excerpt of AFdb or MIT-BIH arrhythmia/200 e.g., have it analyzed by a practitioner and you will find a.s. that annotations are poor or wrong or missing and most cases are statistically unbalanced with too few patients. 

So cool question and I am also interested in knowing about the alternatives including private.

If this helps in any way:

IITG Multuvaribility Phase-I Speaker Recognition database contains two sessions speech data from 100 speakers collected in an office environment using Digital Voice Recorder  which have 44.1k sampling rate. But it is paid database.

IITG MV Phase-II database has 104 speakers but the environment is not clean.

Thanks Feras, this is not quite what I am looking for however. By near misses, I mean: “... an event/situation in which a negative outcome could have occurred but did not, either by chance or because the problem was identified and corrected before a negative outcome occurred.” - Crane, 2015. 

For example, a situation where a surgeon nearly operates on the wrong leg, but the problem is caught in time. 

Elasticsearch could be your perfect option. Elastic search has three main component Elastic search engine,  Logstach and Kibana. Elastic  search  engine will easily digest your text information. The Kibana component is a visualization tool that will allow you search for things quickly. The only issue here is the learning curve to get it installed. Check it out here https://www.elastic.co/products/elasticsearch

Why not use Bioinformatics tools that allow you to suit your needs rather than a dbms and then write codes. GenScripts in one such tool but its not free. Other options include COPIA, EMBOSS (European Molecular Biology Open Software Suite), FASTA, and BLAST ( Basic Local Alignment Search Tool). They all serve different purpose hence you need to deep-six them.

Try Abstract Plus, developed by CDC USA, it is a cancer registry tool, stable and very helpful for single institution application.

In addition to the above answers, you might see if you are able to create a project through the Zooniverse platform (https://www.zooniverse.org/), as they now have a "build your own project" feature. It is doesn't fit your needs, perhaps contact the developers,whom are located in the US and UK from my understanding. Alternatively, you could explore if local NGOs or museums would have interest in your project and helping you develop your own database that citizen scientists can contribute. An Australian example of a project collective supported by a museum is the Bowerbird project (bowerbirds famously collect things for the nesting sites, so the project name is metaphorical rather than literal: http://www.bowerbird.org.au/). It might also be worth checking SciStarter (http://scistarter.com/index.html), which is a project finder, to see if anyone else is doing a similar project you could collaborate with.

Thank you, Uvernes. I will pass along this link to my neighbor who is working on this problem with the Department of Corrections here. He is Rich Jacobs ( richjacobs12@gmail.com ). Ultimately a nationwide network of links is needed, available to released prisoners, and for companies and agencies committed to successful reentry into society. The initial step would be developing or expanding what is a available locally to a wider region. Much of what is available may be outdated or limited in scope.

Thanks for your understanding and further elaboration 

for the sake of curiosity, does the light reached over Mars is different? I think the difference is only the atmospheric condition which may lead to some specific changes in spectral signature. lets wait together 

Cheers!

You can refer some tools for that. or 

You can request your colleagues and friends to draw the outline or border of the regions. Then you can integrate all the outlines and form the ground truth. I do not remember the tool for drawing outline manually. you can google it.

I think that in the near future they will have to deal with some sort of consistency issues specially for critical applications. Most business databases (transactional) works with strong consistency but lack the high performance of NoSQL databases. Trading of performance with consistency is not a solution. some attempts have been done to add transactions to NoSQL databases such as http://www.vldb.org/pvldb/vol6/p1434-dey.pdf in VLDB2013. I believe it will come to a point in the future that there will be transactions (consistency) without losing the high performance of NoSQL databases.

REPLACE should do the trick: http://dev.mysql.com/doc/refman/5.0/en/string-functions.html#function_replace

If you got a table 'MyTable' with a column 'MyName' then the SQL statement would be:

look at our recent experimentation in a conversion of SQL to NoSQL and see the results. We suggest that some guidelines would be helpful because the current developers have years of SQL thinking

Caché, ConceptBase, Db4o, GemStone/S, NeoDatis ODB, ObjectDatabase++, ObjectDB, Objectivity/DB, ObjectStore, ODABA, OpenAccess, OpenLink Virtuoso, Perst, Picolisp, siaqodb, Twig, Versant Object Database, WakandaDB, Zope Object Database.

Use the MODEM Architeture Description Method and define the Configuration Baselines of your system elements in your Enterprise System Release. Do all this together with the Requirement Profiles for each element. Then you have defined your design of a Capability Package (CP)

/P

Last year Roger Urgeles published this pretty extensive database of landslides in the Mediterranean:

Hello, you need to put a little bit more effort that just using Matlab. I would suggest using a bash script or Python and an API like this one https://www.robowhois.com/ (It has 500 credits - searches for free) to do your task. You can do it with Matlab, but you will have to hack stuff together to get it to talk to the API. I hope this is useful to you!

Hello,

There is a free SQLf plugin for Postgresql developed by a french team (Pilgrim/IRISA) with collaboration with Postgresql french group. It is accessible on "https://github.com/postgresqlf/PostgreSQL_f".

The plugin allows users defining fuzzy predicates such as "cheap", "low", "recent" etc. and using them in SQL statements like :

SELECT DISTINCT make, name, model, price, mileage, year, get_mu() as mu

FROM annoncesauto

WHERE (price ~= 'very cheap') && (mileage ~= 'low') && (age ~= 'recent')

ORDER BY mu DESC LIMIT 15;

The documentation is unfortunately in french but as it is about a technical topic enriched with several SQL examples, its translatation into english would not be so difficult.

I think that this pluging can be a good start to figure out how fuzzy databases work.

Enjoy,

Nouredine.

you must contact some medical lab for a number of patient datasets. In such scenarios, the research students contact such organizations at university level.

Hello, since the previous answers didn't mention it, I think you should look at anonymization techniques. The point is that even if you remove all obviously identifying fields, like names, unique IDs and so forth, it may still be possible to uniquely identify records by the association of particular fields. For example, Sweeney demonstrated about 10 years ago that 87% of the american population could be uniquely identified by an aggregation of Gender, Age and Zipcode where they lived.

Narayanan and Shmatikov also could deanonymize data published by netflix for research purposes, data that had been previously anonymized by removal of identifying fields.

If you are interested in this, I would suggest you look at these specific terms: k-anonymization, l-diversity, t-closeness. These all apply to manipulations of database records. You lose in accuracy of the data, but you gain in privacy. If you want to keep the data as exact as possible but only for aggregate queries, then you might be better served by other techniques like data perturbation and permutation of sensitive data.

Perhaps you are looking for information regarding Return on Investment (ROI) to guide a proposal to develop or implement DBMS? ROI estimates should include both tangible financial costs and returns and intangible costs and benefits. As mentioned by Venkateswara above, this really does depend on the sector you are in and the type of system and purpose of the system. ROI seems to be much more easily measured in commercial and financial sectors, but much more difficult to evaluate eg in the health sector, where there is still debate about the benefits of HIT. The benefits derived from a database system (especially if this is not also part of an operational/transactional system) will also depend on the ability to use the stored data afterwards, so benefit can be confounded by poor management and use after implementation. Try looking up ROI for information systems in the relevant business area.

On the basis of my experience with MongoDb, I agree with Martin Holzhauer's observation that standardization runs counter to the special-purpose use of NoSql databases.

Also, the notion that standardization would be needed to maintain ACID properties seems no to apply to NoSql -- currently these properties are enforced by programmers as needed.

An SD card is a storage device typically used by cameras (de facto standard now). A smart card is an older moniker for a credit or debit card (for example) with a chip.

It depends on the number of dimensions you need to index and the volume of data you need to handle. If the number of dimensions is not too large (<20) an index such as the k-d-tree would be fine, but if data volume is large, you would need to use a paginated version of it, such as our Q-tree which has been developed by our research group (gim.unex.es) at the University of Extremadura. However, if the number of dimensions is larger than that, you could consider access methods that fight against the curse of dimensionality such as the VA-File or Localy Sensitive Hashing. Also it depends on the kind of searches you are planning to run against the data. All the mentioned structured incorporate nearest neighbor searches.