ExtremeDB: A Unified Web Repository of Extremophilic Archaea and Bacteria

Majhi, Manash Chandra; Behera, Abhisek K.; Kulshreshtha, Niha Mohan; Mahmooduzafar,; Kumar, Ram; Kumar, Anil

doi:10.1371/journal.pone.0063083

Cited by 11 publications

(8 citation statements)

References 13 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Very few computational resources have been developed in the area of microbial diversity and related fields. These databases are more specialized and have focused on a specific microbe or niche such as fungal diversity and evolution (PHYMYCO-DB [16] ), extremophiles (ExtremeDB [17] ), human oral microbiome (HOMD [18] ), or pathogenic bacteria (PATRIC [19] ). Some databases have focused mainly on the molecular data of microbes, such as the CORE [20] , LAMP [21] , PolysacDB [22] , MiST 2.2 [23] , EzTaxon-e [11] , RDP [24] , and GenBank databases.…”

Section: Resultsmentioning

confidence: 99%

NEMiD: A Web-Based Curated Microbial Diversity Database with Geo-Based Plotting

Bhattacharjee

Joshi

2014

PLoS ONE

View full text Add to dashboard Cite

The majority of the Earth's microbes remain unknown, and that their potential utility cannot be exploited until they are discovered and characterized. They provide wide scope for the development of new strains as well as biotechnological uses. The documentation and bioprospection of microorganisms carry enormous significance considering their relevance to human welfare. This calls for an urgent need to develop a database with emphasis on the microbial diversity of the largest untapped reservoirs in the biosphere. The data annotated in the North-East India Microbial database (NEMiD) were obtained by the isolation and characterization of microbes from different parts of the Eastern Himalayan region. The database was constructed as a relational database management system (RDBMS) for data storage in MySQL in the back-end on a Linux server and implemented in an Apache/PHP environment. This database provides a base for understanding the soil microbial diversity pattern in this megabiodiversity hotspot and indicates the distribution patterns of various organisms along with identification. The NEMiD database is freely available at www.mblabnehu.info/nemid/.

show abstract

Section: Resultsmentioning

confidence: 99%

NEMiD: A Web-Based Curated Microbial Diversity Database with Geo-Based Plotting

Bhattacharjee

Joshi

2014

PLoS ONE

View full text Add to dashboard Cite

show abstract

“…Since these microorganisms live in a biologically competitive environment for space and nutrients, they have developed mechanisms of defence against competitors and predators for their own survival, synthesising secondary metabolites of great value in pharmaceutical and biotechnological applications [91,92]. The advances in genome sequencing of extremophilic microorganisms have allowed us to provide a comprehensive understanding of their applications [93][94][95]. Moreover, microbes with large genomes, usually inhabiting complex harsh environments, can produce a vast array of secondary metabolites [96,97].…”

Section: Biotechnological Potential Of Prokaryotes Inhabiting Dhabsmentioning

confidence: 99%

“…Mar. Drugs 2020, 18, 91 7 of 32 [93][94][95]. Moreover, microbes with large genomes, usually inhabiting complex harsh environments, can produce a vast array of secondary metabolites [96,97].…”

Section: Biotechnological Potential Of Prokaryotes Inhabiting Dhabsmentioning

confidence: 99%

Deep Hypersaline Anoxic Basins as Untapped Reservoir of Polyextremophilic Prokaryotes of Biotechnological Interest

2020

View full text Add to dashboard Cite

Deep-sea hypersaline anoxic basins (DHABs) are considered to be among the most extreme ecosystems on our planet, allowing only the life of polyextremophilic organisms. DHABs’ prokaryotes exhibit extraordinary metabolic capabilities, representing a hot topic for microbiologists and biotechnologists. These are a source of enzymes and new secondary metabolites with valuable applications in different biotechnological fields. Here, we review the current knowledge on prokaryotic diversity in DHABs, highlighting the biotechnological applications of identified taxa and isolated species. The discovery of new species and molecules from these ecosystems is expanding our understanding of life limits and is expected to have a strong impact on biotechnological applications.

show abstract

“…In the experiments, we implement the proposed logbased recovery algorithm on the eXtremeDB embedded database [19], and compare it with the traditional recovery method and the method in eXtremeDB. The experiments contain a small database, and the operations include insert, delete, and modification.…”

Section: Experimental Settingmentioning

confidence: 99%

Research on recovery strategy in embedded real-time main memory databases

Tan

Yin

2016

J Embedded Systems

View full text Add to dashboard Cite

In order to recover data from embedded real-time main memory databases effectively and efficiently, this paper proposes a real-time log-based recovery approach. With respect to the real-time requirement in embedded systems, we classify the consistency in real-time main memory databases into data and transaction consistencies, analyze them theoretically, design rules for correct recovery strategy, and propose real-time log-based recover algorithms for different types of transactions. The experiments show that the proposed approach is more effective and efficient than methods in both traditional and eXtremeDB database systems.Keywords: Embedded system, Real-time main memory database, Recovery strategy, Consistency ReviewWith the development of embedded systems, the application of databases in embedded systems [1] is a hotspot in both industry and academia. Embedded systems work in an environment without manual intervention, so when a fault occurs in these systems, they need to diagnose the fault and recover it automatically all by themselves [2]. The main memory databases [3,4] can reduce the I/O operations greatly while running, and satisfy the real-time requirement of embedded systems, so the databases implemented in embedded systems usually work in the main memory.In real-time main memory databases [5][6][7], the main copy of database works in the volatile RAM, and the data is very vulnerable, so the recovery is necessary. Meantime, the I/O operations in real-time main memory databases are few, and recovery is the only part that affects the I/O performance, so the performance of recovery is critical for real-time main memory databases [8,9]. While recovering from a fault, real-time main memory databases need to satisfy multiple constraints [10,11], and this pose a huge challenge for designing reasonable recovering strategies.Checkpoint or memory snapshots [12, 13] is a commonly used program recovery strategy, but the overhead of storing states of running program is very high, and it is not suitable for embedded applications. In addition, the logs in embedded systems record the behaviors of embedded systems, and researchers use different logs to design different recovery strategies, such as partition log [14], real-time log [15], remote log [16], and operation log [17]. However, these strategies only take the requirement of real-time into consideration, and ignore other specific requirements in embedded systems, so they cannot be applied to the embedded environment efficiently. In addition, the method proposed in [13], studied the recovery strategy in main-memory, but the method is based on virtual memory snapshots. In order to improve real-time ability, Levy and Silberschatz [18] proposed an incremental recovery strategy in mainmemory database.In this paper, we analyze the consistency constraints in embedded real-time main memory databases from the perspectives of both data and transaction. Then we design some rules that an efficient recovery strategy must obey in embedded real-time main memory database...

show abstract

ExtremeDB: A Unified Web Repository of Extremophilic Archaea and Bacteria

Cited by 11 publications

References 13 publications

NEMiD: A Web-Based Curated Microbial Diversity Database with Geo-Based Plotting

NEMiD: A Web-Based Curated Microbial Diversity Database with Geo-Based Plotting

Deep Hypersaline Anoxic Basins as Untapped Reservoir of Polyextremophilic Prokaryotes of Biotechnological Interest

Research on recovery strategy in embedded real-time main memory databases

Contact Info

Product

Resources

About