Data intensive analysis tasks such as analyzing genomic data increasingly call for more and more sophisticated levels of programming proficiency in researchers. Desktop and internet based applications have been designed to create workflows which will help address this problem. However many are unintuitive and have limited access to the high performance computing (HPC) infrastructure needed for large datasets.
In a recently published article published in Source Code for Biology and Medicine, Hunter et al. present Yabi; an open source software system designed to provide transparent access to high performance computing. Hunter and colleagues describe their new application as ‘a workflow engine that solves the problem of workflow deployment across disparate legacy HPC resources’. Designed to provide a more intuitive workflow environment, Yabi is a web-based user service intended to target an audience which may not have specialized programming skills.
Yabi employs a three tier architecture; a front end user interface, ‘middleware’ responsible for process management and ‘resource manager’ which computes resources to middleware. This structure allows the system to interface with a variety of different storage and computer systems facilitating easier access to storage resources and preventing ‘data lock-in’.
One of Yabi’s most interesting features is that it allows
users to design their own workflows by selecting each tool they wish to use and
then completing that tool’s mandatory inputs. The user can then name and save
the workflow they have just created which is then stored as part of an audit
trail and may be reused at a later date. Already being used by a number of
research communities in fields like genomics, transcriptomics and proteomics,
Yabi is ‘domain agnostic’ and can be used to service many different life
With the introduction of Yabi, Hunter et al. hope to move the complexity involved in accessing HPC away
from the individual researcher and enable scientists without specialized
computer knowledge access to HPC power. To download Yabi for yourself please
click the following link to the authors website; https://ccg.murdoch.edu.au/yabi/login/?next=/yabi/.
You can also follow the Yabi project on Twitter.
Kazi za uchambuzi wa data kama vile kuchambua data ya genomic inahitaji zaidi na zaidi ngazi za utaalam wa programu katika watafiti. Desktop na mtandao msingi maombi wamekuwa iliyoundwa kuunda workflows ambayo itasaidia kushughulikia tatizo hili. Hata hivyo, wengi ni unintuitive na kuwa na upatikanaji mdogo kwa high utendaji kompyuta (HPC) miundombinu zinahitajika kwa ajili ya seti kubwa ya data. Katika makala iliyochapishwa hivi karibuni katika Code Source kwa Biolojia na Tiba, Hunter et al. Yabi; mfumo wa programu ya chanzo wazi iliyoundwa kutoa upatikanaji wa uwazi kwa kompyuta ya utendaji wa juu. Hunter na wenzake kuelezea maombi yao mpya kama "mjini workflow kwamba kutatua tatizo la workflow kupelekwa katika rasilimali tofauti urithi HPC". Iliundwa kutoa mazingira ya kazi ya moja kwa moja zaidi, Yabi ni huduma ya mtumiaji wa wavuti iliyokusudiwa kulenga watazamaji ambao wanaweza kuwa hawana ujuzi wa programu maalum. Yabi anatumia tatu ngazi usanifu; mbele mwisho user interface, <unk>middleware<unk> wajibu wa mchakato wa usimamizi na <unk>resource meneja<unk> ambayo computes rasilimali kwa middleware. Muundo huu inaruhusu mfumo wa interface na aina mbalimbali za kuhifadhi na mifumo ya kompyuta kuwezesha upatikanaji rahisi kwa rasilimali kuhifadhi na kuzuia "data lock-katika". Moja ya Yabi ya vipengele ya kuvutia ni kwamba inaruhusu watumiaji kubuni workflows yao wenyewe kwa kuchagua kila chombo wanataka kutumia na kisha kukamilisha chombo kwamba lazima pembejeo. Kisha mtumiaji anaweza jina na kuhifadhi workflow wao tu umba ambayo ni kisha kuhifadhiwa kama sehemu ya kufuatilia kufuatilia na inaweza kutumika tena katika tarehe ya baadaye. Tayari kutumika na idadi ya jamii ya utafiti katika nyanja kama vile genomics, transcriptomics na proteomics, Yabi ni <unk>domain agnostic<unk> na inaweza kutumika kwa huduma ya maisha mengi tofauti na kuanzishwa kwa Yabi, Hunter et al. "Kama matokeo, watafiti watapata uwezo wa kuondoa ""ugumu"" unaohusika katika kupata HPC kutoka kwa mtafiti mmoja na kuwezesha wanasayansi bila ujuzi wa kompyuta maalum kupata nguvu ya HPC." Ili kuweza ku-download kwa ajili yako mwenyewe, tafadhali bonyeza kiungo kifuatacho kwenye tovuti ya mwandishi: https: www.murdock.edu.au yabi.org Unaweza pia kufuata mradi wa Yabi kwenye Twitter.