Soft Computing, Artificial Intelligence, Fuzzy Logic & Genetic Algorithm in Bioinformatics

Abstract Soft computing is creating several possibilities in bioinformatics, especially by generating low-cost, low precision (approximate), good solutions. Bioinformatics is an interdisciplinary research area that is the interface between the biological and computational sciences. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, structural biology, software engineering, data mining, image processing, modeling and simulation, discrete mathematics, control and system theory, circuit theory, and statistics. Despite of a high number of techniques specifically dedicated to bioinformatics problems as well as many successful applications, we are in the beginning of a process to massively integrate the aspects and experiences in the different core subjects such as biology, medicine, computer science, engineering, and mathematics. Recently the use of soft computing tools for solving bioinformatics problems have been gaining the attention of researchers because of their ability to handle imprecision, uncertainty in large and complex search spaces. The paper will focus on soft computing paradigm in bioinformatics with particular emphasis on integrative research

Tecnologías bioinformáticas para el análisis de secuencias de ADN

La solución del problema biológico e informático del procesamiento de grandes volúmenes de datos que contienen información de las secuencias de ADN requiere métodos computacionales avanzados, buscando así una optimización del tiempo en el que se realiza este proceso actualmente y permitiendo colaborar en un futuro con las investigaciones de las ciencias biológicas. Se pretende conocer cuáles son las herramientas bioinformáticas específicas que permitan el avance de los estudios científicos en el análisis de secuencias de ADN.Solving the biological and computering problem about processing of large volumes of data that contains DNA sequences information requires advanced Computaciónal methods, searching an optimization of time that this process is done now and allowing collaborating on a future research life sciences. This article pretendes to know what are the specific bioinformatics tools that allows the advance of scientific studies in the DNA secuence analysis

Ecological and population genomics of the wild yellow-necked mouse, Apodemus flavicollis

Species belonging to the genus Apodemus are one of the most common and broadly distributed small mammals in the Palearctic, making them ideal for studying ecological and evolutionary processes in natural systems. Although much research has focused on the ecology of Apodemus sp., relatively little is known about the evolutionary processes which govern their natural variation in the wild. This is, in part, due to the limitations of de novo genomic research in traditionally non-model organisms. However, recent advances in high-throughput library preparation techniques such as RADseq, have made non-model organisms more accessible for genome wide analyses. This thesis shows how a modified RADseq protocol (quaddRAD) can be used to conduct ecological and evolutionary genomics research in a large population of wild yellow-necked mice, Apodemus flavicollis, that is subject to highly seasonal conditions. I show how a high quality genomic dataset of 21,011 SNPs can be generated using quaddRAD, and discuss the rationale behind the methodology in detail. I then use the genotypes to construct a multi-generational pedigree, and describe the population’s demography, fitness and allele frequency dynamics over time. I find significant variation in the genetic contributions of mice to each generation, where by the end of the study, 53.6% of the sampled population was descended from a single individual. Contrary to the expected high levels of inbreeding and low genetic diversity in such a population, I find it is largely panmictic, which suggests a large degree of connectivity to nearby populations allowing genetic rescue through high levels of migration and gene flow. Finally, I show how heterothermic responses, which reduce an individuals energy budget by up to 65% under harsh conditions, are not only highly variable in the population, but also highly heritable. This suggests heterothermy could be subject to natural selection. I show that heterothermic responses form two distinct thermal strategies in the morphospace, which may be the result of different modes of selection acting on the population to maintain significant natural variation. This thesis shows the viability of quaddRAD for large scale genomics research in wild Apodemus sp., to cement their role as a model organism for ecological and evolutionary genomics research

Resource enhancement and sustainable aquaculture practices in Southeast Asia: challenges in responsible production of aquatic species : proceedings of the international workshop on resource enhancement and sustainable aquaculture practices in Southeast Asia 2014 (RESA)

The conference was held in order to promote and augment regional initiatives on resource enhancement and sustainable aquaculture practices, and to contribute to poverty alleviation, livelihood and food security in Southeast Asia. The contributions of the selected participants during the conference which are contained in this volume are cited individually.The Government of Japan through the Trust Fund Programs of the SEAFDEC Secretariat provided financial support for the conduct of the International Workshop on Resource Enhancement and Sustainable Aquaculture practices in Southeast Asia in March 2014 in Iloilo, Philippines, as well as, the publication of this proceedings. The editors also acknowledge the efforts of the Publication Review Committee of SEAFDEC/AQD especially Dr. Relicardo M. Coloso, Dr. Maria Lourdes Cuvin-Aralar, Dr. Evelyn Grace de Jesus Ayson, Dr. Rolando Pakingking and Dr. Myrna B. Teruel for reviewing the draft of the proceedings prior to its publication. Thanks are also due Ms. Imee S. Hacla for the copy-editing and layout.Collapse All Expand AllFOREWORDMESSAGESKEYNOTE ADDRESSPREFACEACKNOWLEDGEMENTSPLENARY PAPERSIs small-hold tropical aquaculture in a genetic plunge towards extinction?Roger W. DoyleRapid adaptation to a new environment: is it reversible?Hitoshi ArakiCOUNTRY PAPERSCambodiaCurrent status of sustainable aquaculture in CambodiaOuch LangJapanStatus of resource enhancement and sustainable aquaculture practices in JapanKoichi Okuzawa, Takayuki Takebe, Narisato Hirai and Kazumasa IkutaMalaysiaStatus of resource management and aquaculture in MalaysiaAishah YusoffMyanmarInland fisheries resource enhancement and conservation practices in MyanmarHtun TheinPhilippinesThe Philippine National Aquasilviculture ProgramRomeo E. Dieta and Florida C. DietaViet NamGood aquaculture practices (VietGAP) and sustainable aquaculture development in Viet NamNguyen Thi Bang TamLao PDRCountry status on sustainable aquaculture in Lao PDRThongkhoun KhonglalianeSingaporeCurrent status of aquaculture in SingaporeNeo Chin HengIndonesiaSustainable aquaculture and resources enhancement inIndonesiaSetiawan Soetardjo and Irham AdhityaThailandMilkish: new choice for aquaculture in ThailandPrapat KosawatpatCONTRIBUTED PAPERSAssessment of humphead wrasse (Cheilinus undulatus), spawningaggregations and declaration of marine protected area as strategy for enhancement of wildstocksFilemon G. Romero and Akkil S. InjaniStock assessment of christian crabs (Charybdis feriatus, Linnaeus,1758)in San Miguel bayPlutomeo M. Nieves, Nelson R. Olfindo and Aldrin Mel MacaleAbalone aquaculture for stock enhancement and community livelihoodproject in northern Palawan, PhilippinesBenjamin J. GonzalesSocial preparations towards community-based approach to stockenhancement in Sagay Marine Reserve, PhilippinesNerissa D. Salayo, Raisa Joy G. Castel, Dianne Hope M. Tormon, Rafael T. Barrido, MarieFrancesJ. Nievales and Teruo AzumaCommunity-based shrimp stock enhancement for coastal socio-ecological restoration in the PhilippinesJon Altamirano, Hisashi Kurokura, Nerissa Salayo, Didi Baticados, Jee Grace Suyo and Satoshi IshikawaBFAR-CHED Philippine National Aquasilviculture Program (PNAP) in BataanRudy C. Flores, Felicisima E. Tungol, Abraham S Antonio, Elizabeth D. Medairos and Jonathan M.SalasMarine fish hatchery: developments and future trendsClarissa L. Marte and Joebert D. ToledoHatchery management techniques for tiger-tail seahorse (Hippocampus comes)Shelah Mae B. Ursua and Teruo AzumaUpdates on the seed production of mud crabEmilia T. Quinitio, Fe D. Parado-Estepa, Joana Joy Huervana and Michael Ray BurlasMarker-aided genetic stock management: prospects in Philippine Aquatic Biodiversity conservation and aquacultureMaria Rowena R. Romana-Eguia, Minoru Ikeda and Akihiro KijimaFeed formulation for sustainable aquacultureRelicardo M. ColosoPotential of cowpea (Vigna unguiculata L.) meal as an alternativeprotein source in diets for giant freshwater prawn (Macrobrachium rosenbergii, de Man 1879)Frolan A. Aya, Maria Lourdes Cuvin-Aralar and Relicardo M. ColosoApplication of the United States Soybean Export Council program's soy-optimized floating feeds and low volume, high density cage aquaculture technologiesLevy Loreto L. Manalac, Michael Cremer, Hsiang Pin Lan and Lukas ManomaitisUtilization of sensors and SMS technology to remotely maintain thelevelof dissolved oxygen, salinity and temperature of fishpondsRodrigo C. Munoz, Reynan P. Calderon, Rudy C. Flores, Sisenando C. Masangcap, Jayson P.Angelesand Mark ColentavaReaching the poor through aquaculture: The case of technologyadoptionin rural communities at west central PhilippinesDidi B. BaticadosMarine biodiversity at the SEAFDEC/AQD research stations in IloiloandGuimaras, PhilippinesTeodora Uy BagarinaoTargeting essential gene utilizing RNA interference to protect theailing shrimp/prawn industry against WSSVJassy Mary S. Lazarte and Mary Beth B. ManingasABSTRACTS OF ORAL PRESENTATIONSSEAFDEC/AQD stock enhancement initiatives: releasestrategiesMa. Junemie Hazel Lebata-Ramos, Ellen Flor Doyola-Solis, Rema Sibonga, Joemel Sumbing, Jeff Bogart Abroguena, August Santillan and Mark DimzonResponsible shrimp culture through ecological approachEleonor A. TendenciaEstimation of energy budget of sea cucumber, Holothuria scabra, in integrated multi-trophic aquacultureSatoshi Watanabe, Masashi Kodama, Zenith Gaye A. Orozco, Joemel G. Sumbing, Schedar Rose M. Novilla and Ma. Junemie Hazel Lebata-RamosPost-larval rearing strategies in sandish (Holothuria scabra) cultureMarie Frances Nievales, Rema Sibonga and Harold FiguradoInduced breeding of giant trevally, maliputo (Caranx ignobilis)Ma. Theresa M. Mutia, Frederick B. Muyot and Myleen L. MagistradoSeed production of the blue swimming crab (Portunus pelagicus)Nonita S. Cabacaba and Jimmy E. SalamidaPotential genetic impacts of hatchery-based resource enhancementZubaida U. BasiaoGood aquaculture practices (GAqP): setting directions for harmonized regional standards - the Philippine experienceMark F. Matubang and Nelson A. LopezThe importance of mangroves to capture and culture fisheriesJurgenne H. PrimaveraStock enhancement? Why botherJose InglesABSTRACTS OF POSTER PRESENTATIONSResource assessment of sea cucumber in northern Iloilo, central PhilippinesPerry A. Alpasan and Romy A. BillonesOptimization of feeding and growth conditions for hatchery-bred larvae of indigenous Philippine silver perch, Leiopotherapon plumbeus (Perciformes: Terapontidae)Julie Andrea Añano, Frolan Aya, Mark Nell Corpuz and Maria Rowena R. Romana-EguiaDevelopment of a simple, rapid, cost-effective diagnostic kit for WSSVPocholo Mari T. Arabit, Amalea Dulcene D. Nicolasora, Patrick Ellis Z. Go, Christopher Marlowe A. Caipang and Mary Beth B. ManingasLarval rearing of silver therapon (Leiopotherapon plumbeus) in outdoor tanksFrolan A. Aya, Vicar Stella N. Nillasca, Mark Nell C. Corpuz and Luis Maria B. GarciaPreliminary trials on the effects of weaning and larval diets on survival and growth of silver therapon (Leiopotherapon plumbeus) larvaeFrolan A. Aya , Vicar Stella N. Nillasca and Luis Maria B. GarciaA preliminary study on the diagnosis of coral reef healthiness and establishment of coral replenishment technologyTeruo Azuma, Jemar Jed Roble Tan, Jacques Zarate, Jon Altamirano, Joey Gatus and Filipina SottoPreliminary assessment of the abundance and fishery of snapping shrimp (Alpheus sp.) in Calape, Bohol, PhilippinesJomel G. Baobao, Maria Danesa S. Rabia and Ernesto C. RulidaModelling the impact of different stress agents on Holothurian immunityLiudmila S. DolmatovaGrowth and survival of nile tilapia (Oreochromis niloticus) juveniles fed diets with varying levels of irradiated chitosanKristine Gonzales, Mark Nell Corpuz and Maria Rowena R. Romana-EguiaPerceptions on the effects of maritime activities on the Philippine aquatic ecosystemEnrique Java, Teresita Cruz and Isidro Yonggue HernandezPreliminary trials on the optimization of hormone dosages for induced breeding of Philippine silver perch, Leiopotherapon plumbeusMark Archei O. Javier, Frolan A. Aya and Maria Rowena R. Romana-EguiaDistribution and abundance of hard clam shells Meretrix meretrix along the coastal areas of Panguil bay, Lanao del Norte, PhilippinesCelestina Q. Jumawan , Rheino B. Palma and Renalyn O. SiaGrowth performance of brackishwater enhanced selected tilapia (BEST) reared in brackishwater pondsAnecito V. Labastida, Celestina Q. Jumawan, Antonio A. Abogado, Rheino B. Palma and Jerome J. SabilloFirst record of Laem-Singh virus in black tiger shrimp (Penaeus monodon) in the PhilippinesChristian Albert M. Cruz, Precious C. dela Cruz, Paul Christian D. Alcala, Florenz Giovanni M. Tagle, Erickson S. Santos, Mudjekeewis D. Santos and Mary Beth B. ManingasReproductive biology of christian crabs (Charybdis feriatus, Linnaeus, 1758) in San Miguel Bay, PhilippinesPlutomeo M. Nieves, Nelson R. Olfindo and Aldrin Mel MacaleShrimp metabolism: The roles of lactate dehydrogenase (c31), glycogen phosphorylase (c34) and protein kinase (PK) as revealed by RNA interferenceMaria Violeta R. Tare, Hidehiro Kondo, Ikuo Hirono and Mary Beth B. ManingasSUMMARY OF THE WORKSHOPANNEXESANNEX 1. Workshop CommitteesANNEX 2. Directory of Participants</div

Investigating and Writing Achitectural History: Subjects, Methodologies and Frontiers.

The volume contains the abstracts and full texts of the 157 papers and position statements presented and discussed at the III EAHN (European Architectural History) International Meeting, Torino 19-21 June 201